diff --git a/bin/partis b/bin/partis index a5fbcd9f8..269fdda89 100755 --- a/bin/partis +++ b/bin/partis @@ -37,6 +37,7 @@ import partis.seqfileopener as seqfileopener from partis.partitiondriver import PartitionDriver from partis.clusterpath import ClusterPath import partis.paircluster as paircluster +import partis.disjointgrouper as disjointgrouper from partis.parametercounter import ParameterCounter from partis.corrcounter import CorrCounter from partis.waterer import Waterer @@ -1660,6 +1661,8 @@ subconfig = collections.OrderedDict(( ('get-linearham-info', {'func' : run_partitiondriver, 'help' : 'Write input file for linearham (to --linearham-info-fname), using a previous partis output (--outfname) file as input.'}), ('update-meta-info', {'func' : run_partitiondriver, 'help' : 'Read existing output files and update their info from --input-metafnames, i.e. if your input meta info changed but you don\'t want to rerun everything. Also updates --queries-to-include info.'}), ('write-fake-paired-annotations', {'func' : run_partitiondriver, 'help' : 'Read paired output from --paired-outdir, and write \'fake\' annotations by concatenating h and l seqs to file in the same dir (useful e.g. for phylo method input).'}), + ('disjoint-group', {'func' : disjointgrouper.run_disjoint_group, 'help' : 'Split sequences into disjoint groups by cdr3 length, writing per-group fastas and a manifest yaml to --outdir. Auto-runs sw annotation if --parameter-dir is not set.'}), + ('assemble-groups', {'func' : disjointgrouper.run_assemble_groups, 'help' : 'Validate and merge per-group partition outputs from disjoint grouping. Reads manifest from --disjoint-dir, reconciles germline info, checks sequence count invariants and uid uniqueness, and writes a single merged partition yaml per locus. Use --no-merge-output to keep per-group files separate for large datasets.'}), # deprecated actions: ('view-annotations' , {'func' : run_partitiondriver, 'help' : 'Mostly deprecated: Print annotations from an existing old-style annotation output csv (for current yaml output files, use \'view-output\').'}), ('view-partitions' , {'func' : run_partitiondriver, 'help' : 'Mostly deprecated: Print partitions from an existing old-style partition output csv (for current yaml output files, use \'view-output\').'}), @@ -1800,6 +1803,10 @@ subargs['plot-partitions'].append({'name' : '--seed-loci', 'kwargs' : {'help' : subargs['get-linearham-info'].append({'name' : '--linearham-info-fname', 'kwargs' : {'help' : 'yaml file to which to write linearhmam input information'}}) +subargs['disjoint-group'].append({'name' : '--disjoint-dir', 'kwargs' : {'help' : 'Working directory for disjoint grouping. Step 1 writes manifest + per-group fastas here, step 2 writes per-group partition yamls here, step 3 reads from here.'}}) +subargs['assemble-groups'].append({'name' : '--disjoint-dir', 'kwargs' : {'help' : 'Working directory for disjoint grouping (same directory used for disjoint-group step 1 and partition step 2).'}}) +subargs['assemble-groups'].append({'name' : '--no-merge-output', 'kwargs' : {'action' : 'store_true', 'help' : 'Skip writing merged single-yaml output; keep per-group partition files separate (for large datasets where a single multi-GB yaml is impractical).'}}) + sub_arg_groups = {'subset-partition' : ['partition'], 'subset-annotate' : ['annotate']} # actions that use the args of other actions (i.e. their need to be merged, e.g. 'subset-partition' needs access to all the args of 'partition') def get_arg_names(actions): # return set of all arg names (in the form they appear in args.__dict__) for the specified actions diff --git a/partis/disjointgrouper.py b/partis/disjointgrouper.py new file mode 100644 index 000000000..a55d14a2f --- /dev/null +++ b/partis/disjointgrouper.py @@ -0,0 +1,336 @@ +from __future__ import absolute_import, division, unicode_literals +from __future__ import print_function +import os +import sys +import json +import yaml +import collections +import shutil + +from . import utils +from . import glutils +from . import paircluster + +# ---------------------------------------------------------------------------------------- +def group_sequences_by_cdr3_length(annotation_list): + # group uids and their input sequences by cdr3 length from sw annotation list + # each annotation has unique_ids (list) and input_seqs (list, parallel), plus cdr3_length (int) + groups = collections.OrderedDict() # {cdr3_length : [{'name': uid, 'seq': seq}, ...]} + n_failed = 0 + for line in annotation_list: + if 'cdr3_length' not in line or line['cdr3_length'] is None: + n_failed += len(line['unique_ids']) + continue + c3len = line['cdr3_length'] + if c3len not in groups: + groups[c3len] = [] + for uid, seq in zip(line['unique_ids'], line['input_seqs']): + groups[c3len].append({'name' : uid, 'seq' : seq}) + if n_failed > 0: + print(' %s %d sequences had no cdr3_length and were excluded from grouping' % (utils.color('yellow', 'warning'), n_failed)) + return groups, n_failed + +# ---------------------------------------------------------------------------------------- +def write_group_fastas(groups, outdir, locus): + # write per-group fasta files, one per cdr3 length, streaming writes + # returns list of group info dicts for the manifest + group_infos = [] + for gid, (c3len, seqfos) in enumerate(sorted(groups.items())): + group_dir = '%s/groups/cdr3-%d' % (outdir, c3len) + fasta_path = '%s/%s.fa' % (group_dir, locus) + utils.mkdir(fasta_path, isfile=True) + with open(fasta_path, 'w') as ffile: + for sfo in seqfos: + ffile.write('>%s\n%s\n' % (sfo['name'], sfo['seq'])) + rel_fasta_path = 'groups/cdr3-%d/%s.fa' % (c3len, locus) + group_infos.append({ + 'group_id' : gid, + 'cdr3_length' : c3len, + 'locus' : locus, + 'sequence_count' : len(seqfos), + 'fasta_path' : rel_fasta_path, + 'partition_path' : None, + }) + print(' group %d: cdr3 length %d, %d sequences -> %s' % (gid, c3len, len(seqfos), rel_fasta_path)) + return group_infos + +# ---------------------------------------------------------------------------------------- +def write_manifest(group_infos, outdir, loci, total_input, n_failed, parameter_dir=None): + # write manifest yaml to outdir + manifest = { + 'version-info' : {'partis-yaml' : 0.2}, + 'grouping-info' : { + 'method' : 'cdr3-length', + 'loci' : loci, + 'total_input_sequences' : total_input, + 'total_grouped_sequences' : total_input - n_failed, + 'failed_sequences' : n_failed, + 'parameter_dir' : parameter_dir, + }, + 'groups' : group_infos, + 'assembly' : { + 'status' : 'pending', + 'merged_output_path' : None, + 'validation' : { + 'gene_lists_consistent' : None, + 'uids_unique' : None, + 'sequence_count_preserved' : None, + }, + }, + } + manifest_path = '%s/manifest.yaml' % outdir + utils.mkdir(manifest_path, isfile=True) + with open(manifest_path, 'w') as mfile: + yaml.dump(manifest, mfile, width=400, default_flow_style=False) + print(' wrote manifest to %s' % manifest_path) + return manifest + +# ---------------------------------------------------------------------------------------- +def read_manifest(manifest_path): + # read and validate manifest yaml + if not os.path.exists(manifest_path): + raise Exception('manifest file does not exist: %s' % manifest_path) + with open(manifest_path) as mfile: + manifest = yaml.safe_load(mfile) + for required_key in ['version-info', 'grouping-info', 'groups', 'assembly']: + if required_key not in manifest: + raise Exception('missing required key \'%s\' in manifest %s' % (required_key, manifest_path)) + for ginfo in manifest['groups']: + for required_key in ['group_id', 'cdr3_length', 'locus', 'sequence_count', 'fasta_path']: + if required_key not in ginfo: + raise Exception('missing required key \'%s\' in group entry in manifest %s' % (required_key, manifest_path)) + return manifest + +# ---------------------------------------------------------------------------------------- +def validate_sequence_count(manifest): + # verify that sum of group sequence counts equals total_grouped_sequences + total_grouped = manifest['grouping-info']['total_grouped_sequences'] + group_sum = sum(g['sequence_count'] for g in manifest['groups']) + if group_sum != total_grouped: + raise Exception('sequence count mismatch: sum of group counts %d does not equal total_grouped_sequences %d' % (group_sum, total_grouped)) + total_input = manifest['grouping-info']['total_input_sequences'] + n_failed = manifest['grouping-info']['failed_sequences'] + if total_grouped + n_failed != total_input: + raise Exception('sequence count mismatch: total_grouped %d + failed %d does not equal total_input %d' % (total_grouped, n_failed, total_input)) + print(' sequence count validated: %d grouped + %d failed = %d total' % (total_grouped, n_failed, total_input)) + +# ---------------------------------------------------------------------------------------- +def get_sw_cache_path(parameter_dir, locus): + import glob + # try per-locus subdir first (paired data), then flat (unpaired) + for search_dir in ['%s/%s' % (parameter_dir, locus), parameter_dir]: + fnames = glob.glob(search_dir + '/sw-cache*.yaml') + if len(fnames) > 0: + return fnames[0] + raise Exception('sw cache not found in %s/%s/ or %s/' % (parameter_dir, locus, parameter_dir)) + +# ---------------------------------------------------------------------------------------- +def get_loci(args): + if args.paired_loci: + return utils.sub_loci(args.ig_or_tr) + else: + return [args.locus] + +# ---------------------------------------------------------------------------------------- +def find_partis_cmd(): + # find the partis binary, same logic as find_cmd() in bin/partis + if shutil.which('partis'): + return 'partis' + partis_dir = os.path.dirname(os.path.dirname(os.path.abspath(__file__))) + partis_path = '%s/bin/partis' % partis_dir + if os.path.exists(partis_path): + return partis_path + raise Exception('could not find partis binary in PATH or at %s' % partis_path) + +# ---------------------------------------------------------------------------------------- +def get_infname_for_locus(args, locus): + # get the input file path for a given locus + if args.paired_loci: + if args.paired_indir is not None: + # try both .yaml and .fa suffixes (same logic as getifn() in run_all_loci) + yfn, ffn = [paircluster.paired_fn(args.paired_indir, locus, suffix=sx) for sx in ['.yaml', '.fa']] + if os.path.exists(yfn) and os.path.exists(ffn): + raise Exception('both %s and %s exist, not sure which to use' % (yfn, ffn)) + return yfn if os.path.exists(yfn) else ffn + elif args.infname is not None: + raise Exception('--paired-loci with --infname requires locus splitting (use --paired-indir with pre-split files, or run split-loci.py first)') + else: + raise Exception('--paired-indir or --infname must be set for auto-caching with --paired-loci') + else: + return args.infname + +# ---------------------------------------------------------------------------------------- +def get_parameter_dir_for_locus(args, locus): + # get the per-locus parameter dir (paired data uses subdirs per locus) + if args.paired_loci: + return '%s/%s' % (args.parameter_dir, locus) + else: + return args.parameter_dir + +# ---------------------------------------------------------------------------------------- +def auto_cache_parameters(args, loci): + # run cache-parameters --only-smith-waterman for each locus that does not have an sw cache + partis_cmd = find_partis_cmd() + for ltmp in loci: + try: + get_sw_cache_path(args.parameter_dir, ltmp) + print(' %s: sw cache already exists in %s' % (ltmp, args.parameter_dir)) + continue + except Exception: + pass # no sw cache found, need to run cache-parameters + infname = get_infname_for_locus(args, ltmp) + pdir = get_parameter_dir_for_locus(args, ltmp) + print(' %s: running cache-parameters --only-smith-waterman (input: %s, parameter-dir: %s)' % (ltmp, infname, pdir)) + cmd = '%s cache-parameters --infname %s --parameter-dir %s --locus %s --only-smith-waterman' % (partis_cmd, infname, pdir, ltmp) + if hasattr(args, 'n_procs') and args.n_procs is not None: + cmd += ' --n-procs %d' % args.n_procs + if hasattr(args, 'is_simu') and args.is_simu: + cmd += ' --is-simu' + utils.simplerun(cmd) + +# ---------------------------------------------------------------------------------------- +def run_disjoint_group(args): + if args.disjoint_dir is None: + raise Exception('--disjoint-dir must be set for disjoint-group') + has_input = args.infname is not None or (hasattr(args, 'paired_indir') and args.paired_indir is not None) + if not has_input and args.parameter_dir is None: + raise Exception('--infname (or --paired-indir with --paired-loci) or --parameter-dir must be set for disjoint-group') + + outdir = args.disjoint_dir + loci = get_loci(args) + + # set default parameter dir if not provided (same convention as run_partitiondriver in bin/partis) + if args.parameter_dir is None: + instr = args.paired_indir if args.paired_loci and hasattr(args, 'paired_indir') and args.paired_indir is not None else args.infname + args.parameter_dir = '_output/%s' % utils.getprefix(instr).replace('/', '_') + print(' note: --parameter-dir not set, so using default: %s' % args.parameter_dir) + + # auto-trigger sw annotation if sw cache does not exist + auto_cache_parameters(args, loci) + + print(' running disjoint-group on %s with parameter dir %s' % (' '.join(loci), args.parameter_dir)) + + all_group_infos = [] + total_input = 0 + total_failed = 0 + for ltmp in loci: + sw_cache_path = get_sw_cache_path(args.parameter_dir, ltmp) + print(' reading sw cache for %s from %s' % (ltmp, sw_cache_path)) + glfo, annotation_list, _ = utils.read_yaml_output(sw_cache_path, dont_add_implicit_info=True) + groups, n_failed = group_sequences_by_cdr3_length(annotation_list) + n_seqs = sum(len(seqfos) for seqfos in groups.values()) + n_failed + total_input += n_seqs + total_failed += n_failed + print(' %s: %d sequences in %d cdr3 length groups (%d failed)' % (ltmp, n_seqs - n_failed, len(groups), n_failed)) + group_infos = write_group_fastas(groups, outdir, ltmp) + all_group_infos.extend(group_infos) + + manifest = write_manifest(all_group_infos, outdir, loci, total_input, total_failed, parameter_dir=args.parameter_dir) + validate_sequence_count(manifest) + +# ---------------------------------------------------------------------------------------- +def get_partition_paths_by_locus(manifest, manifest_dir): + # collect and verify partition file paths grouped by locus + paths_by_locus = collections.OrderedDict() + missing_partitions = [] + for ginfo in manifest['groups']: + ppath = ginfo.get('partition_path') + if ppath is None: + missing_partitions.append(ginfo['group_id']) + continue + full_ppath = '%s/%s' % (manifest_dir, ppath) + if not os.path.exists(full_ppath): + missing_partitions.append(ginfo['group_id']) + continue + if os.path.getsize(full_ppath) == 0: + raise Exception('partition file is empty for group %d: %s' % (ginfo['group_id'], full_ppath)) + ltmp = ginfo['locus'] + if ltmp not in paths_by_locus: + paths_by_locus[ltmp] = [] + paths_by_locus[ltmp].append(full_ppath) + if len(missing_partitions) > 0: + raise Exception('partition files missing for %d groups: %s' % (len(missing_partitions), missing_partitions)) + return paths_by_locus + +# ---------------------------------------------------------------------------------------- +def validate_assembly(manifest, manifest_dir): + # validate uid uniqueness and sequence counts by reading each group one at a time + # (does not load all annotations into memory at once, so scales to large datasets) + all_uids = set() + total_seqs = 0 + paths_by_locus = get_partition_paths_by_locus(manifest, manifest_dir) + for ltmp, yaml_list in paths_by_locus.items(): + for ppath in yaml_list: + glfo, annotation_list, _ = utils.read_yaml_output(ppath, dont_add_implicit_info=True) + for line in annotation_list: + for uid in line['unique_ids']: + if uid in all_uids: + raise Exception('duplicate uid %s found across groups' % uid) + all_uids.add(uid) + total_seqs += sum(len(line['unique_ids']) for line in annotation_list) + expected = manifest['grouping-info']['total_grouped_sequences'] + if total_seqs != expected: + raise Exception('sequence count mismatch after assembly: found %d uids in partition files, expected %d' % (total_seqs, expected)) + print(' assembly validation passed: %d unique sequences across %d groups' % (total_seqs, len(manifest['groups']))) + +# ---------------------------------------------------------------------------------------- +def assemble_merged_output(manifest, manifest_dir, disjoint_dir): + # merge per-group partition yamls into single per-locus output + # cannot use utils.merge_yamls() because per-group partition files have different numbers + # of partition steps (from hierarchical agglomeration), and merge_yamls() asserts they match. + # instead, read each file, extract the best partition and annotations, reconcile germlines, + # and write a combined output. + from .clusterpath import ClusterPath + assembled_dir = '%s/assembled' % disjoint_dir + utils.mkdir(assembled_dir) + paths_by_locus = get_partition_paths_by_locus(manifest, manifest_dir) + for ltmp, yaml_list in paths_by_locus.items(): + outfname = '%s/partition-%s.yaml' % (assembled_dir, ltmp) + print(' merging %d partition files for %s -> %s' % (len(yaml_list), ltmp, outfname)) + merged_annotation_list = [] + merged_partition = [] + merged_glfo = None + for infname in yaml_list: + glfo, annotation_list, cpath = utils.read_yaml_output(infname, dont_add_implicit_info=True) + print(' %d sequences in %d clusters from %s' % (sum(len(l['unique_ids']) for l in annotation_list), len(annotation_list), infname)) + # reconcile germline info + if merged_glfo is None: + merged_glfo = glfo + elif glfo is not None: + merged_glfo, name_mapping = glutils.get_merged_glfo(glfo, merged_glfo) + utils.update_gene_names_in_annotation_list(merged_annotation_list, name_mapping) + merged_annotation_list += annotation_list + # take only the best partition from each group + if cpath is not None and cpath.i_best is not None: + merged_partition += cpath.partitions[cpath.i_best] + # build a single-entry cluster path with the combined best partitions + merged_cpath = ClusterPath() + merged_cpath.add_partition(merged_partition, logprob=0., n_procs=1) + utils.write_annotations(outfname, merged_glfo, merged_annotation_list, utils.annotation_headers, + partition_lines=merged_cpath.get_partition_lines(), dont_write_git_info=True) + manifest['assembly']['merged_output_path'] = 'assembled/' + +# ---------------------------------------------------------------------------------------- +def run_assemble_groups(args): + if args.disjoint_dir is None: + raise Exception('--disjoint-dir must be set for assemble-groups') + + manifest_path = '%s/manifest.yaml' % args.disjoint_dir + print(' running assemble-groups from %s' % manifest_path) + manifest = read_manifest(manifest_path) + manifest_dir = os.path.dirname(os.path.abspath(manifest_path)) + + validate_assembly(manifest, manifest_dir) + manifest['assembly']['validation']['uids_unique'] = True + manifest['assembly']['validation']['sequence_count_preserved'] = True + + if args.no_merge_output: + manifest['assembly']['status'] = 'validated' + print(' --no-merge-output: skipping merged output write (per-group files remain separate)') + else: + assemble_merged_output(manifest, manifest_dir, args.disjoint_dir) + manifest['assembly']['status'] = 'merged' + + with open(manifest_path, 'w') as mfile: + yaml.dump(manifest, mfile, width=400, default_flow_style=False) + print(' updated manifest') diff --git a/partis/processargs.py b/partis/processargs.py index ff867bed7..34fe1b59d 100644 --- a/partis/processargs.py +++ b/partis/processargs.py @@ -12,7 +12,7 @@ def get_dummy_outfname(workdir, locus=None): return '%s/XXX-dummy-simu%s.yaml' % (workdir, '-'+locus if locus is not None else '') -actions_not_requiring_input = ['simulate', 'view-output', 'merge-paired-partitions', 'view-annotations', 'view-partitions', 'view-cluster-annotations', 'plot-partitions', 'view-alternative-annotations', 'get-selection-metrics', 'get-linearham-info', 'write-fake-paired-annotations'] +actions_not_requiring_input = ['simulate', 'view-output', 'merge-paired-partitions', 'view-annotations', 'view-partitions', 'view-cluster-annotations', 'plot-partitions', 'view-alternative-annotations', 'get-selection-metrics', 'get-linearham-info', 'write-fake-paired-annotations', 'disjoint-group', 'assemble-groups'] # ---------------------------------------------------------------------------------------- # split this out so we can call it from both bin/partis and bin/test-germline-inference.py diff --git a/test/paired/ref-results/disjoint-group-new-data/assembled/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/assembled/partition-igh.yaml new file mode 100644 index 000000000..870d9ae5e --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/assembled/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": 0.0, "n_clusters": 48, "n_procs": 1, "partition": [["AAACGGGAGAAACGCC-1_contig_1"], ["AAAGATGCACGGACAA-1_contig_2"], ["AAACCTGAGCGCCTTG-1_contig_2"], ["AAACGGGTCCGTTGTC-1_contig_2"], ["AAACGGGAGGCCCTTG-1_contig_1"], ["AAACCTGCATTACCTT-1_contig_2"], ["AAACCTGGTAACGCGA-1_contig_1"], ["AAACCTGGTGAACCTT-1_contig_2"], ["AAACCTGTCCGGCACA-1_contig_2"], ["AAAGATGAGCTGAACG-1_contig_2"], ["AAAGATGCAATGTAAG-1_contig_4"], ["AAACCTGCAAATACAG-1_contig_1"], ["AAACCTGTCGGAAACG-1_contig_2"], ["AAACGGGAGATAGCAT-1_contig_1"], ["AAAGATGAGACTAAGT-1_contig_2"], ["AAAGATGCACGACGAA-1_contig_2"], ["AAAGATGCAGCGTCCA-1_contig_1"], ["AAACCTGAGAGACGAA-1_contig_2"], ["AAACCTGCAGTGAGTG-1_contig_1"], ["AAACCTGCATCGACGC-1_contig_1"], ["AAACCTGTCATCTGCC-1_contig_2"], ["AAACGGGAGATCCGAG-1_contig_1"], ["AAACGGGAGCACACAG-1_contig_2"], ["AAACGGGAGGGAGTAA-1_contig_2"], ["AAACGGGAGGTAGCTG-1_contig_2"], ["AAACCTGGTTACGCGC-1_contig_1"], ["AAACCTGTCATATCGG-1_contig_1"], ["AAACCTGTCATCGCTC-1_contig_1"], ["AAAGATGCACCAGCAC-1_contig_1"], ["AAAGATGCATCGTCGG-1_contig_1"], ["AAACGGGCATGACATC-1_contig_2"], ["AAAGATGCAATGTAAG-1_contig_3"], ["AAACCTGCATCTACGA-1_contig_1"], ["AAACCTGGTTCAGTAC-1_contig_2"], ["AAAGATGAGGCGCTCT-1_contig_1"], ["AAAGATGGTATAATGG-1_contig_1"], ["AAACCTGGTCTTGCGG-1_contig_2"], ["AAACGGGGTTGTACAC-1_contig_2"], ["AAACCTGCAGAGCCAA-1_contig_2"], ["AAACCTGGTCAACATC-1_contig_1"], ["AAACGGGAGTCATCCA-1_contig_1"], ["AAACGGGGTACAAGTA-1_contig_2"], ["AAACCTGAGTGAACAT-1_contig_2"], ["AAACGGGAGCGTTGCC-1_contig_2"], ["AAAGATGAGGACCACA-1_contig_2"], ["AAACCTGCAGGGTTAG-1_contig_2"], ["AAACCTGTCCGGCACA-1_contig_3"], ["AAACCTGTCTGGCGAC-1_contig_1"]]}], "events": [{"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGAAACGCC-1_contig_1"], "invalid": false, "v_gene": "IGHV3-74*01", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ4*02", "cdr3_length": 30, "mature_cdr3_lengths": [30], "mut_freqs": [0.06936416184971098], "n_mutations": [24], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGTAACCTCCGGATTCACCTTCAGTAGCTACTGGATGAACTGGGTCCGCCAAGTTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATCCTAATGGAGATTACAAAAACTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTATATCTGCAAATGAACAGTCTGGGAGTCGAGGACACAGCTATATATTACTGTGCAAGGGAGGGGTGGGGTGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCGG"], "has_shm_indels": [false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGAGGGGTGGGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-74*01": 1.0}, "d_per_gene_support": {"IGHD1-26*01": 0.3474119780591844, "IGHD2-21*01": 0.239648755444251, "IGHD2-15*01": 0.20105154789523053, "IGHD3-3*01": 0.19788980440739046, "IGHD3-16*03": 0.013997914193956247}, "j_per_gene_support": {"IGHJ4*02": 0.999999515548499, "IGHJ5*02": 4.844515142301888e-07}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 9, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGG", "dj_insertion": "G", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 312}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCACGGACAA-1_contig_2"], "invalid": false, "v_gene": "IGHV4-31*03", "d_gene": "IGHD1-1*01", "j_gene": "IGHJ3*02", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGAGGAAAATGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGAGGAAAATGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-31*03": 1.0}, "d_per_gene_support": {"IGHD1-1*01": 0.36441620754047893, "IGHD1-14*01": 0.22906198452970422, "IGHD1-7*01": 0.20492327519278372, "IGHD1-20*01": 0.1911932395003912, "IGHD3-3*01": 0.010405293236645737}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 4, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "AA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 321}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGAGCGCCTTG-1_contig_2"], "invalid": false, "v_gene": "IGHV3-30*04", "d_gene": "IGHD4-17*01", "j_gene": "IGHJ3*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.022535211267605635], "n_mutations": [8], "input_seqs": ["NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTACCTATGATATGCACTGGGTCCGCCAGGCTCCAGGCGAGGGGCTGGAATGGGTGGCAGTTATATCCTATGATGGAAGTAATAAATACCACGCAGACTCCGTGAAGGGCCGATTCATCATCTCCAGAGACAATTCCAGGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGTTTCGACTACCATAGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGTTTCGACTACCATAGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-30*04": 0.9999998897034378, "IGHV3-33*01": 1.1029655873674258e-07}, "d_per_gene_support": {"IGHD4-17*01": 0.7578913626706082, "IGHD3-22*01": 0.17837481780053802, "IGHD1-7*01": 0.02994394261997817, "IGHD1-26*01": 0.02754615755973515, "IGHD3-9*01": 0.006243719349139227}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 3, "d_5p_del": 10, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTTC", "dj_insertion": "CATAG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGTCCGTTGTC-1_contig_2"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD7-27*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGGGCAACTGGGGATCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGGGCAACTGGGGATCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD7-27*01": 0.9995072138925739, "IGHD1-20*01": 0.00013780569013004058, "IGHD1-1*01": 0.00013400815420798297, "IGHD6-13*01": 0.0001124738387770488, "IGHD1-7*01": 0.00010849842431122407}, "j_per_gene_support": {"IGHJ4*02": 0.9999988503513109, "IGHJ5*02": 1.149648689502121e-06}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGGC", "dj_insertion": "TC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGGCCCTTG-1_contig_1"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD3-16*03", "j_gene": "IGHJ4*02", "cdr3_length": 42, "mature_cdr3_lengths": [42], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGTTTATCGGAAGAGCCGACTCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGTTTATCGGAAGAGCCGACTCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD3-16*03": 0.9310442101738194, "IGHD1-14*01": 0.04633032725224545, "IGHD2-15*01": 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["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGCCGGCGTATTACTATGGTTCGGGGCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGCCGGCGTATTACTATGGTTCGGGGCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-66*01": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 0.9999895277899583, "IGHD3-22*01": 1.047221003997173e-05}, 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["NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGTTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTACTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGGTGACGCTGATTCGGGGAATTATCTTGGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGGTGACGCTGGTTCGGGGAGTTATCTTGGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-48*02": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 0.9997213334674824, "IGHD7-27*01": 0.0001278167826033714, "IGHD5-24*01": 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["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCATTGTCTCTGGTGGCCCCATCAGCAGTGGTAGTTACTCCTGGGGCTGGATCCGCCAGCCCCCACGGAAGGGGCTGGAGTGGCTTGGGGCTATCTATAATACTGGGAGATCTTACTACAACCCGTCTCTCAAGAGTCGCGTCACCATATCCGTAGACACGTCAAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCCGCAGACACGGCTATATATTACTGCGCGAGGTCAGAACGTATAGCAGTGGATCGTACCCCACGGGGCACGGAATATTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGGTCAGAACGTATAGCAGTGGCTGGTACCCCACGGGGCACGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9821070803271689, "IGHD6-13*01": 0.017516010449585572, "IGHD3-22*01": 0.0003697927170610881, "IGHD6-6*01": 6.983565650314765e-06, "IGHD2-15*01": 1.3294053240762605e-07}, "j_per_gene_support": {"IGHJ4*02": 0.9999997630828258, "IGHJ5*02": 2.369171732344157e-07}, "v_3p_del": 3, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTCAGAAC", "dj_insertion": "CCCACGGGGCACG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 342}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCAATGTAAG-1_contig_3"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ2*01", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.005361930294906166], "n_mutations": [2], "input_seqs": ["NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGACGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGACAGGGGGGCTACTCTGAAAACTATTCATTAAAGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGACAGGGGAGCTACTCTGAAAACTATTCATTAAAGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD1-26*01": 0.8209763296529342, "IGHD3-22*01": 0.12742707980879137, 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["NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACCACATGAACTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTGGTAGTAGTGGTAGTACCATATATTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAAGGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGGGCTCCCCTTATTACTATGGTTCGGGGAGTTATTACAACTTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGGGCTCCCCTTATTACTATGGTTCGGGGAGTTATTATAACTTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-11*01": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 1.0}, "j_per_gene_support": {"IGHJ4*02": 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["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACCCTACTATGATAGTAGTGGTTATTACTTGACCGTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "has_shm_indels": [false], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACCCTACTATGATAGTAGTGGTTATTACTTGACCGTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ3*02": 1.0}, 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"has_shm_indels": [false], "naive_seq": "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGGGCTGTGGTGGTGATTGCTGGCGAGGACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-18*01": 1.0}, "d_per_gene_support": {"IGHD2-21*01": 0.9999757627804391, "IGHD2-15*01": 1.0712778919927556e-05, "IGHD3-22*01": 9.416602177096833e-06, "IGHD3-3*01": 4.104004976441703e-06, "IGHD3-9*01": 3.8334746047425575e-09}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 3, "d_5p_del": 7, "d_3p_del": 5, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGC", "dj_insertion": "GGCGAGG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 345}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGGTATAATGG-1_contig_1"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ4*02", "cdr3_length": 60, "mature_cdr3_lengths": [60], "mut_freqs": [0.03723404255319149], "n_mutations": [14], "input_seqs": ["NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGACTTCTGGATACGCCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAATCCTAACAGTGGTGGCACAATCTATGCACAGGACTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAACTGAGCAGTCTGAGATCTGACGACACGGCCGTCTATTACTGTGCGAGAGCTTATTCCTATGATACTAGTGGTTATTCCTTGGTTCCCTATGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGCTTATTACTATGATAGTAGTGGTTATTACTTGGTTCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ4*02": 0.9999988564592003, "IGHJ5*02": 1.1435408007416749e-06}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 2, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CT", "dj_insertion": "TGGTTCC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 345}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], 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"CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGACGACCAGTTAACTGCATAGCAGCTCGTCCATGTATTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD6-6*01": 0.8369257634822812, "IGHD6-13*01": 0.16067109270932736, "IGHD6-19*01": 0.0020041326486766047, "IGHD7-27*01": 0.00037155787968004556, "IGHD1-20*01": 2.745328003210877e-05}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 2, "d_5p_del": 4, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CGACCAGTTAACTGC", "dj_insertion": "ATGTAT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], 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"CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGGCACCGAGGATATTGTAGTGGTGGTAGCTGCGTAGGGTCACGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD2-15*01": 0.999963012960405, "IGHD2-21*01": 3.6987039601488806e-05}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 6, "j_5p_del": 18, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GCACCG", "dj_insertion": "GTAGGGTCAC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 345}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], 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"NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGATCTTCCAATACTATGCTATGGTTCGGGGAGTTATTCCCCGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 0.9999999999985363, "IGHD3-16*03": 1.4659259871385777e-12}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 2, "d_5p_del": 6, "d_3p_del": 5, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCTTCCAATACTATG", "dj_insertion": "CCCC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 351}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTCAACATC-1_contig_1"], "invalid": false, "v_gene": "IGHV4-4*02", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ6*02", "cdr3_length": 66, "mature_cdr3_lengths": [66], "mut_freqs": [0.028795811518324606], "n_mutations": [11], "input_seqs": ["NNNCAGGTGCAACTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGACATCTATCATAGTGGGAGCAGCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTTGACATGTCCAAGAACCAGTTGTCCCTGCACTTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGGTCCCCGGCGAACTATTACTATGCTTCGGGGTATCTACCCTCTTGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGGTCCCCGGCGAACTATTACTATGGTTCGGGGTATCTACCCTCTTGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-4*02": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 0.9999868460063215, "IGHD3-22*01": 1.2977478135069948e-05, "IGHD3-3*01": 1.7547063077071915e-07, "IGHD6-13*01": 7.666435509412171e-10, "IGHD3-9*01": 2.782472096374846e-10}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 12, "j_5p_del": 18, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTCCCCGGCGAAC", "dj_insertion": "TATCTACCCTCTT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 351}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGTCATCCA-1_contig_1"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ5*02", "cdr3_length": 66, "mature_cdr3_lengths": [66], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACACCGGGGGGAATTCGATTACTATGGTTCGGGGAGTTTCAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACACCGGGGGGAATTCGATTACTATGGTTCGGGGAGTTTCAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 1.0}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 8, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGGGGGGAATTCG", "dj_insertion": "T", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 351}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGGTACAAGTA-1_contig_2"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ5*02", "cdr3_length": 66, "mature_cdr3_lengths": [66], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATTGTTCAGGCGATTTTTGGAGTGGTTATTATCGATACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATTGTTCAGGCGATTTTTGGAGTGGTTATTATCGATACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9999999818677737, "IGHD3-9*01": 1.8132226392770897e-08}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 3, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTGTTCAGG", "dj_insertion": "CGAT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 351}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGAGTGAACAT-1_contig_2"], "invalid": false, "v_gene": "IGHV3-11*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ6*02", "cdr3_length": 69, "mature_cdr3_lengths": [69], "mut_freqs": [0.13246753246753246], "n_mutations": [51], "input_seqs": ["NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAAACTCTCCTGTGCAGCCTCTGGATTCAGCCTCAACGACTACTATATGACCTGGATTCGCCAACCTCCAGGGAAGGGCCTGCAATGGCTTGCATACATCGATAATGTTGGAACAACCACATACTACGCAGACTCTCTGAGGGGCCGCTTCACCATCTCCAGGGACAACAGCAAAAACTCACTGTATCTGCAAATGGACGGCCTGACAGCCGAGGACACGGCCGTCTATTACTGTGCGCGAGATGGTTATTATGATTTTTGGAGTGGTAAATCAGATTATTATTATGGAATGGACCTCTGGGGCCAAGGGACCACGGTCATCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGATGGGTATTACGATTTTTGGAGTGGTTATTATACCTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-11*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.935947957342859, "IGHD3-10*01": 0.02445084739988633, "IGHD3-22*01": 0.02017908907269661, "IGHD3-9*01": 0.018548703117429254, "IGHD3-16*03": 0.0008734030671530159}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TGG", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 354}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGCGTTGCC-1_contig_2"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ4*02", "cdr3_length": 69, "mature_cdr3_lengths": [69], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCTACGTATTACTATGATAGTAGTGGTTATTACTCGGGTCTGGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCTACGTATTACTATGATAGTAGTGGTTATTACTCGGGTCTGGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ4*02": 0.999999462052865, "IGHJ5*02": 5.379471380916758e-07}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 2, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CTAC", "dj_insertion": "CGGGTCTGGGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 354}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGAGGACCACA-1_contig_2"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD3-16*03", "j_gene": "IGHJ6*02", "cdr3_length": 69, "mature_cdr3_lengths": [69], "mut_freqs": [0.14025974025974025], "n_mutations": [54], "input_seqs": ["NNNCAGGCGCAGCTGGAGGAGTCTGGGGGAGGCCTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGCTTCAGTTTCAGTACATATGTCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCGCTTGTCTCGTCTGACGGCAATGATAAATATTATGCAGACTCAGTGAAGGGCCGCTTCACTATCTCCAGAGACAATTCCAAGAACACTCTGGATCTGCAAATGAACAACATGAGAGGCGAGGACACGGCTGTCTATTACTGTGCGAGTGAACAACCCCTCTGGGGTGACTCCGTTGTCGGTTTCTTTTACTACGGAATGGACGTCTGGGGCCCAGGGACCACGGTCACCGTCTCTTCAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGATTACATTTGGGGGAGTTATCGTTATACCTTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 0.9942215983242617, "IGHV3-30*04": 0.005778401675710008}, "d_per_gene_support": {"IGHD3-16*03": 0.7758896010469405, "IGHD2-21*01": 0.18781533949118226, "IGHD4-17*01": 0.03549526273066466, "IGHD6-19*01": 0.0006036155703397153, "IGHD7-27*01": 0.00019618116084292185}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 7, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "T", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 354}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCAGGGTTAG-1_contig_2"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ6*02", "cdr3_length": 72, "mature_cdr3_lengths": [72], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGAAGGAAGTACTATGATAGTAGTGGTGGCACCTATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGAAGGAAGTACTATGATAGTAGTGGTGGCACCTATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 0.9999999837292323, "IGHD2-15*01": 8.43235270846447e-09, "IGHD6-19*01": 4.600117380528303e-09, "IGHD3-16*03": 2.536336762837154e-09, "IGHD3-3*01": 7.019590715268091e-10}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 2, "d_5p_del": 4, "d_3p_del": 9, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AGGAAG", "dj_insertion": "GGCACCT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 357}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCCGGCACA-1_contig_3"], "invalid": false, "v_gene": "IGHV3-21*01", "d_gene": "IGHD4-17*01", "j_gene": "IGHJ6*02", "cdr3_length": 81, "mature_cdr3_lengths": [81], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATGGGGTGATGTATGACTACGGTGACTACGTCCCTTTGCGGTTTTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATGGGGTGATGTATGACTACGGTGACTACGTCCCTTTGCGGTTTTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-21*01": 1.0}, "d_per_gene_support": {"IGHD4-17*01": 0.9999994326981653, "IGHD3-22*01": 4.809730645322982e-07, "IGHD3-10*01": 8.544648466638764e-08, "IGHD2-21*01": 7.459581866952642e-10, "IGHD3-16*03": 1.3632142939706357e-10}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TGGGGTGATGTA", "dj_insertion": "GTCCCTTTGCGGTTT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 363}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCTGGCGAC-1_contig_1"], "invalid": false, "v_gene": "IGHV1-8*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ5*02", "cdr3_length": 84, "mature_cdr3_lengths": [84], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGGCCGACCCAGCAGCTGGTACTTGGGGCGAATAACCTGGCGGGGTGTCAACACTGACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGGCCGACCCAGCAGCTGGTACTTGGGGCGAATAACCTGGCGGGGTGTCAACACTGACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-8*01": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9997784002751684, "IGHD6-19*01": 0.00021569296404276578, "IGHD6-6*01": 5.629811350480175e-06, "IGHD2-15*01": 2.76894401827468e-07, "IGHD1-1*01": 5.5024222184992535e-11}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGACC", "dj_insertion": "TTGGGGCGAATAACCTGGCGGGGTGTCAACACTG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 366}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/assembled/partition-igk.yaml b/test/paired/ref-results/disjoint-group-new-data/assembled/partition-igk.yaml new file mode 100644 index 000000000..f6c34444c --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/assembled/partition-igk.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-12*01": "GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTCC", "IGKV1-27*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCGAGTCAGGGCATTAGCAATTATTTAGCCTGGTATCAGCAGAAACCAGGGAAAGTTCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAATCAGGGGTCCCATCTCGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATGTTGCAACTTATTACTGTCAAAAGTATAACAGTGCCCCTCC", "IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1-5*01": "GACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGAGTATTAGTAGCTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAGTATAATAGTTATTCTCC", "IGKV1-8*03": "GCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCTCC", "IGKV1-9*01": "GACATCCAGTTGACCCAGTCTCCATCCTTCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGGGCATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGCTTAATAGTTACCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV1D-39*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCC", "IGKV2-24*01": "GATATTGTGATGACCCAGACTCCACTCTCCTCACCTGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTACACAGTGATGGAAACACCTACTTGAGTTGGCTTCAGCAGAGGCCAGGCCAGCCTCCAAGACTCCTAATTTATAAGATTTCTAACCGGTTCTCTGGGGTCCCAGACAGATTCAGTGGCAGTGGGGCAGGGACAGATTTCACACTGAAAATCAGCAGGGTGGAAGCTGAGGATGTCGGGGTTTATTACTGCATGCAAGCTACACAATTTCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV2D-28*01": "GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC", "IGKV3-20*01": "GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTCC", "IGKV4-1*02": "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCCTCC", "IGKV6-21*01": "GAAATTGTGCTGACTCAGTCTCCAGACTTTCAGTCTGTGACTCCAAAGGAGAAAGTCACCATCACCTGCCGGGCCAGTCAGAGCATTGGTAGTAGCTTACACTGGTACCAGCAGAAACCAGATCAGTCTCCAAAGCTCCTCATCAAGTATGCTTCCCAGTCCTTCTCAGGGGTCCCCTCGAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACCCTCACCATCAATAGCCTGGAAGCTGAAGATGCTGCAACGTATTACTGTCATCAGAGTAGTAGTTTACCTCA"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*03": "TGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*04": "TGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-5*01": 261, "IGKV1-9*01": 261, "IGKV3-20*01": 264, "IGKV2-24*01": 276, "IGKV1-33*01": 261, "IGKV1-12*01": 261, "IGKV2D-28*01": 276, "IGKV1-27*01": 261, "IGKV6-21*01": 261, "IGKV3-11*01": 261, "IGKV1D-39*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV4-1*02": 279, "IGKV2-30*01": 276, "IGKV1-8*03": 261}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*04": 8, "IGKJ2*03": 8, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 33, "n_procs": 1, "partition": [["AAACCTGGTAACGCGA-1_contig_2", "AAACGGGAGATAGCAT-1_contig_2", "AAACGGGAGGCCCTTG-1_contig_2"], ["AAACCTGGTCAACATC-1_contig_2"], ["AAAGATGCAATGTAAG-1_contig_2"], ["AAAGATGCATCGTCGG-1_contig_2"], ["AAACCTGAGAGACGAA-1_contig_1"], ["AAACCTGAGCGCCTTG-1_contig_1"], ["AAACCTGCAGAGCCAA-1_contig_1"], ["AAACCTGCAGGGTTAG-1_contig_1"], ["AAACCTGCATCGACGC-1_contig_2"], ["AAACCTGCATTACCTT-1_contig_1"], ["AAACCTGGTCTTGCGG-1_contig_1"], ["AAACCTGGTGAACCTT-1_contig_1"], ["AAACCTGGTTACGCGC-1_contig_2"], ["AAACCTGTCATATCGG-1_contig_2", "AAACGGGAGTCATCCA-1_contig_2"], ["AAACCTGTCGGAAACG-1_contig_1"], ["AAACGGGAGAAACGCC-1_contig_2", "AAAGATGCAATGTAAG-1_contig_1"], ["AAACGGGAGCGTTGCC-1_contig_1"], ["AAACGGGGTTGTACAC-1_contig_1"], ["AAACGGGTCGTGACAT-1_contig_1"], ["AAAGATGAGCTGAACG-1_contig_1"], ["AAAGATGAGGACCACA-1_contig_1"], ["AAAGATGCACCAGCAC-1_contig_2"], ["AAAGATGGTATAATGG-1_contig_2"], ["AAACCTGAGTGAACAT-1_contig_1"], ["AAACCTGCAGTGAGTG-1_contig_2"], ["AAACCTGTCATCTGCC-1_contig_1"], ["AAACCTGTCCGGCACA-1_contig_1"], ["AAACGGGAGCACACAG-1_contig_1"], ["AAAGATGCACGACGAA-1_contig_1"], ["AAAGATGCACGGACAA-1_contig_1"], ["AAACCTGGTTCAGTAC-1_contig_1"], ["AAACCTGTCCGAAGAG-1_contig_1"], ["AAAGATGAGACTAAGT-1_contig_1"]]}], "events": [{"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["AAACCTGGTAACGCGA-1_contig_2", "AAACGGGAGATAGCAT-1_contig_2", "AAACGGGAGGCCCTTG-1_contig_2"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 30, "mature_cdr3_lengths": [30, 30, 30], "mut_freqs": [0.0, 0.003134796238244514, 0.0], "n_mutations": [0, 1, 0], "input_seqs": ["NNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "NNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATCATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "NNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "has_shm_indels": [false, false, false], "naive_seq": "NNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGKV3-15*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ1*01": 1.0}, "v_3p_del": 6, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 276, "j": 303}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTCAACATC-1_contig_2"], "invalid": false, "v_gene": "IGKV3-11*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 30, "mature_cdr3_lengths": [30], "mut_freqs": [0.0219435736677116], "n_mutations": [7], "input_seqs": ["NNNNNNNNNNNNNNNGAAATTGTGTTGACACAATCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTTCTTAGCCTGGTATCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTCTGATACATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCATCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTCGCAACTGGCCCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "has_shm_indels": [false], "naive_seq": "NNNNNNNNNNNNNNNGAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV3-11*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 0.9999981868643554, "IGKJ1*01": 1.813135641141175e-06}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 276, "j": 303}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCAATGTAAG-1_contig_2"], "invalid": false, "v_gene": "IGKV2D-28*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 30, "mature_cdr3_lengths": [30], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "has_shm_indels": [false], "naive_seq": "GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV2D-28*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ1*01": 1.0}, "v_3p_del": 7, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 276, "j": 303}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCATCGTCGG-1_contig_2"], "invalid": false, "v_gene": "IGKV1D-39*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 30, "mature_cdr3_lengths": [30], "mut_freqs": [0.025078369905956112], "n_mutations": [8], "input_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAACTTTTTACATTGGTATCAGCAAAAACCAGGGAAAGCCCCTAACCTCCTGATCTATGCTGCATCCAGCTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTATGCAACTTACTACTGTCAACAGACTTACAGTACCCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "has_shm_indels": [false], "naive_seq": "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV1D-39*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 0.9999999556825837, "IGKJ3*01": 4.4317418443606924e-08}, "v_3p_del": 5, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 276, "j": 303}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": 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["GCCTTCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCGTCTGAGGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGCCATTAGTCGTACTTTAGCCTGGTATCAGCAGAAACCAGGGAAAATTCCTGAACTCCTGATCTCTTATGGCTCCAATTTGGAAAGTGGGGTCCCATCTAGGTTCAGCGGCCATGTATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCGGCCTGGGGATTTTGCAACTTATTTCTGTCAACACTTTAATACTTTCACTCACGAAGTCACTTTCGGCGGAGGGACCAAGGTGGAGATTAAAC"], "has_shm_indels": [false], "naive_seq": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCACGGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV1D-13*02": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 0.9999972063310821, "IGKJ3*01": 2.7936689402730085e-06}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 261, "j": 297}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/assembled/partition-igl.yaml b/test/paired/ref-results/disjoint-group-new-data/assembled/partition-igl.yaml new file mode 100644 index 000000000..b79d8792a --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/assembled/partition-igl.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV1-51*02": "CAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCAGGAACAGCCCCCAAACTCCTCATCTATGAAAATAATAAGCGACCCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGGAACATGGGATAGCAGCCTGAGTGCTGG", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC", "IGLV3-1*01": "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGCA", "IGLV3-19*01": "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATCT", "IGLV3-27*01": "TCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCTCAGGAGATGTACTGGCAAAAAAATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTGCTGGTGATTTATAAAGACAGTGAGCGGCCCTCAGGGATCCCTGAGCGATTCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATCT", "IGLV4-60*03": "CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTAGCTACATCATCGCATGGCATCAGCAGCAGCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAGGTAGTGGAAGCTACAACAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGGGCTGACCGCTACCTCACCATCTCCAACCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCA", "IGLV7-46*04": "CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGG", "IGLV8-61*01": "CAGACTGTGGTGACCCAGGAGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTTACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGGCTCCACGCACGCTCATCTACAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGAACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTACTGTGTGCTGTATATGGGTAGTGGCATTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"}}, "cyst-positions": {"IGLV8-61*01": 267, "IGLV2-14*04": 267, "IGLV4-60*03": 273, "IGLV2-23*02": 267, "IGLV1-40*01": 267, "IGLV3-1*01": 258, "IGLV1-51*02": 264, "IGLV7-46*04": 267, "IGLV3-27*01": 258, "IGLV3-19*01": 258}, "phen-positions": {"IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 11, "n_procs": 1, "partition": [["AAACCTGTCATCGCTC-1_contig_2", "AAAGATGAGGCGCTCT-1_contig_2", "AAACGGGAGGTAGCTG-1_contig_1"], ["AAACCTGTCTGGCGAC-1_contig_2"], ["AAACGGGTCCGTTGTC-1_contig_1"], ["AAAGATGCAGCGTCCA-1_contig_2"], ["AAACGGGAGGGAGTAA-1_contig_1"], ["AAACGGGCATGACATC-1_contig_1"], ["AAAGATGCACGGACAA-1_contig_3"], ["AAACCTGCAAATACAG-1_contig_2"], ["AAACCTGCATCTACGA-1_contig_2", "AAACGGGAGATCCGAG-1_contig_2", "AAACGGGAGATCCGAG-1_contig_3"], ["AAACCTGTCCGGCACA-1_contig_4"], ["AAACGGGGTACAAGTA-1_contig_1"]]}], "events": [{"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["AAACCTGTCATCGCTC-1_contig_2", "AAAGATGAGGCGCTCT-1_contig_2", "AAACGGGAGGTAGCTG-1_contig_1"], "invalid": false, "v_gene": "IGLV3-1*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33], "mut_freqs": [0.05956112852664577, 0.003134796238244514, 0.006269592476489028], "n_mutations": [19, 1, 2], "input_seqs": ["NNNNNNNNNTCCTATGACCTGACTCAGCCACCCTCCGTGTCCGTGTCCCCAGGCCAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGAGATAAATTTGTTTCCTGGTATGAACAGAGGCCAGGCCAGTCCCCTGTCCTGGTCATCTATCAAGATAGGAAGTGGCCCTCAGGGATCCCTGATCGATTCTCTGGCTCCAAGTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCAATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGTAGTAGTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "NNNNNNNNNTCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGCGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "NNNNNNNNNTCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false, false, false], "naive_seq": "NNNNNNNNNTCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGLV3-1*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ2*01": 0.9908931334814428, "IGLJ3*02": 0.009106866518562785}, "v_3p_del": 5, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "C", "fv_insertion": "NNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 267, "j": 297}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCTGGCGAC-1_contig_2"], "invalid": false, "v_gene": "IGLV7-46*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGGGCCTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGGGCCTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV7-46*04": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.5161803483489827, "IGLJ2*01": 0.4838196516510166}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GCC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 297}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGTCCGTTGTC-1_contig_1"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCCTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCCTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV2-23*02": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ1*01": 1.0}, "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 297}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCAGCGTCCA-1_contig_2"], "invalid": false, "v_gene": "IGLV3-27*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.025078369905956112], "n_mutations": [8], "input_seqs": ["NNNNNNNNNTCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCGCAGGAGATATACTGGCAAAAAGATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTATTGGTGATTTATAAAGACACTGAGCGGCCCTCAGGGATCCCTGAGCGAATCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATAGAGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "NNNNNNNNNTCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCTCAGGAGATGTACTGGCAAAAAAATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTGCTGGTGATTTATAAAGACAGTGAGCGGCCCTCAGGGATCCCTGAGCGATTCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV3-27*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.98680698577856, "IGLJ2*01": 0.013193014221439352}, "v_3p_del": 2, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "NNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 297}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGGGAGTAA-1_contig_1"], "invalid": false, "v_gene": "IGLV8-61*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.03323262839879154], "n_mutations": [11], "input_seqs": ["NNNNNNCAGACTGTGGTGACCCAGGTGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTCACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGACTCCACGCACGCTCATCTATAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGGACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTATTGTTTGCTATATATGCGTAGTGGCGTTTGGGTGTTCGGCGGAGGGACCAGGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "NNNNNNCAGACTGTGGTGACCCAGGAGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTTACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGGCTCCACGCACGCTCATCTACAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGAACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTACTGTGTGCTGTATATGGGTAGTGGCATTTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV8-61*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.9112556727062637, "IGLJ2*01": 0.08874432729372951}, "v_3p_del": 2, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 273, "j": 306}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGCATGACATC-1_contig_1"], "invalid": false, "v_gene": "IGLV4-60*03", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.04154302670623145], "n_mutations": [14], "input_seqs": ["CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTGGTTACTTGATCGCGTGGCATCAGCAGCACCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAAGTAGTGGAATCTACACCAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGCACTGACCGCTACCTCTCCATCTCCAATCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCCTGTGGTCTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTAGCTACATCATCGCATGGCATCAGCAGCAGCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAGGTAGTGGAAGCTACAACAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGGGCTGACCGCTACCTCACCATCTCCAACCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCCTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV4-60*03": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ2*01": 0.9953572783978399, "IGLJ3*02": 0.00464272160216174}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 273, "j": 306}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCACGGACAA-1_contig_3"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.00906344410876133], "n_mutations": [3], "input_seqs": ["NNNNNNCAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGCGTTATAATCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCACTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "NNNNNNCAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV2-23*02": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.9784972680425973, "IGLJ2*01": 0.021502731957398286}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 273, "j": 306}}, {"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["AAACCTGCATCTACGA-1_contig_2", "AAACGGGAGATCCGAG-1_contig_2", "AAACGGGAGATCCGAG-1_contig_3"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39, 39], "mut_freqs": [0.017964071856287425, 0.0029940119760479044, 0.005988023952095809], "n_mutations": [6, 1, 2], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAACACCCAGGCAAAGCCCCCAAACTCGTTATTTATGATGTCAGTAGTCGGCCCTCAGGGGTCTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCGGGGTGTTCGGCGGAGGGACCAAGGTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTAGGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCGAGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false, false, false], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCGGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGLV2-14*04": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.9971097965694344, "IGLJ2*01": 0.002890203430572608}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "G", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 267, "j": 303}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCAAATACAG-1_contig_2"], "invalid": false, "v_gene": "IGLV1-51*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.030211480362537766], "n_mutations": [10], "input_seqs": ["NNNCAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCACGAACAGCCCCCAAACTCCTCATTTACGAAAATAGTGAGCGATTCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGAAACATGGGATGACAGCCTGAGTGCTGGGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCAGGAACAGCCCCCAAACTCCTCATCTATGAAAATAATAAGCGACCCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGGAACATGGGATAGCAGCCTGAGTGCTGGGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV1-51*02": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ2*01": 0.978075111167959, "IGLJ3*02": 0.02192488883204208}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 303}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCCGGCACA-1_contig_4"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV1-40*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ1*01": 1.0}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 303}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGGTACAAGTA-1_contig_1"], "invalid": false, "v_gene": "IGLV3-19*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNNNNTCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [false], "naive_seq": "NNNNNNNNNTCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV3-19*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ2*01": 0.9999737961760137, "IGLJ3*02": 2.620382398641891e-05}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 303}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/igh.fa new file mode 100644 index 000000000..d8caeca25 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/igh.fa @@ -0,0 +1,2 @@ +>AAACGGGAGAAACGCC-1_contig_1 +GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGTAACCTCCGGATTCACCTTCAGTAGCTACTGGATGAACTGGGTCCGCCAAGTTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATCCTAATGGAGATTACAAAAACTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTATATCTGCAAATGAACAGTCTGGGAGTCGAGGACACAGCTATATATTACTGTGCAAGGGAGGGGTGGGGTGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCGG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/igk.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/igk.fa new file mode 100644 index 000000000..2f929e120 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/igk.fa @@ -0,0 +1,12 @@ +>AAACCTGGTAACGCGA-1_contig_2 +GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>AAACCTGGTCAACATC-1_contig_2 +GAAATTGTGTTGACACAATCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTTCTTAGCCTGGTATCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTCTGATACATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCATCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTCGCAACTGGCCCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>AAACGGGAGATAGCAT-1_contig_2 +GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATCATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>AAACGGGAGGCCCTTG-1_contig_2 +GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>AAAGATGCAATGTAAG-1_contig_2 +GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>AAAGATGCATCGTCGG-1_contig_2 +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAACTTTTTACATTGGTATCAGCAAAAACCAGGGAAAGCCCCTAACCTCCTGATCTATGCTGCATCCAGCTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTATGCAACTTACTACTGTCAACAGACTTACAGTACCCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/partition-igh.yaml new file mode 100644 index 000000000..fdf0b6504 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -177.6178579483573, "n_clusters": 1, "n_procs": 1, "partition": [["AAACGGGAGAAACGCC-1_contig_1"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGAAACGCC-1_contig_1"], "invalid": false, "v_gene": "IGHV3-74*01", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ4*02", "cdr3_length": 30, "mature_cdr3_lengths": [30], "mut_freqs": [0.06936416184971098], "n_mutations": [24], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGTAACCTCCGGATTCACCTTCAGTAGCTACTGGATGAACTGGGTCCGCCAAGTTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATCCTAATGGAGATTACAAAAACTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTATATCTGCAAATGAACAGTCTGGGAGTCGAGGACACAGCTATATATTACTGTGCAAGGGAGGGGTGGGGTGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCGG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGAGGGGTGGGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-74*01": 1.0}, "d_per_gene_support": {"IGHD1-26*01": 0.3474119780591844, "IGHD2-21*01": 0.239648755444251, "IGHD2-15*01": 0.20105154789523053, "IGHD3-3*01": 0.19788980440739046, "IGHD3-16*03": 0.013997914193956247}, "j_per_gene_support": {"IGHJ4*02": 0.999999515548499, "IGHJ5*02": 4.844515142301888e-07}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 9, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGG", "dj_insertion": "G", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 312}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/partition-igk.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/partition-igk.yaml new file mode 100644 index 000000000..dd5179ee2 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-30/partition-igk.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-12*01": "GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTCC", "IGKV1-27*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCGAGTCAGGGCATTAGCAATTATTTAGCCTGGTATCAGCAGAAACCAGGGAAAGTTCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAATCAGGGGTCCCATCTCGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATGTTGCAACTTATTACTGTCAAAAGTATAACAGTGCCCCTCC", "IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1-5*01": "GACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGAGTATTAGTAGCTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAGTATAATAGTTATTCTCC", "IGKV1-8*03": "GCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCTCC", "IGKV1-9*01": "GACATCCAGTTGACCCAGTCTCCATCCTTCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGGGCATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGCTTAATAGTTACCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV1D-39*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCC", "IGKV2-24*01": "GATATTGTGATGACCCAGACTCCACTCTCCTCACCTGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTACACAGTGATGGAAACACCTACTTGAGTTGGCTTCAGCAGAGGCCAGGCCAGCCTCCAAGACTCCTAATTTATAAGATTTCTAACCGGTTCTCTGGGGTCCCAGACAGATTCAGTGGCAGTGGGGCAGGGACAGATTTCACACTGAAAATCAGCAGGGTGGAAGCTGAGGATGTCGGGGTTTATTACTGCATGCAAGCTACACAATTTCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV2D-28*01": "GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC", "IGKV3-20*01": "GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTCC", "IGKV4-1*02": "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCCTCC", "IGKV6-21*01": "GAAATTGTGCTGACTCAGTCTCCAGACTTTCAGTCTGTGACTCCAAAGGAGAAAGTCACCATCACCTGCCGGGCCAGTCAGAGCATTGGTAGTAGCTTACACTGGTACCAGCAGAAACCAGATCAGTCTCCAAAGCTCCTCATCAAGTATGCTTCCCAGTCCTTCTCAGGGGTCCCCTCGAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACCCTCACCATCAATAGCCTGGAAGCTGAAGATGCTGCAACGTATTACTGTCATCAGAGTAGTAGTTTACCTCA"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*03": "TGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*04": "TGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-5*01": 261, "IGKV1-9*01": 261, "IGKV3-20*01": 264, "IGKV2-24*01": 276, "IGKV1-33*01": 261, "IGKV1-12*01": 261, "IGKV2D-28*01": 276, "IGKV1-27*01": 261, "IGKV6-21*01": 261, "IGKV3-11*01": 261, "IGKV1D-39*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV4-1*02": 279, "IGKV2-30*01": 276, "IGKV1-8*03": 261}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*04": 8, "IGKJ2*03": 8, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": -432.92731104428947, "n_clusters": 4, "n_procs": 1, "partition": [["AAACCTGGTAACGCGA-1_contig_2", "AAACGGGAGATAGCAT-1_contig_2", "AAACGGGAGGCCCTTG-1_contig_2"], ["AAACCTGGTCAACATC-1_contig_2"], ["AAAGATGCAATGTAAG-1_contig_2"], ["AAAGATGCATCGTCGG-1_contig_2"]]}], "events": [{"has_shm_indels": [false, false, false], "qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["AAACCTGGTAACGCGA-1_contig_2", "AAACGGGAGATAGCAT-1_contig_2", "AAACGGGAGGCCCTTG-1_contig_2"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 30, "mature_cdr3_lengths": [30, 30, 30], "mut_freqs": [0.0, 0.003134796238244514, 0.0], "n_mutations": [0, 1, 0], "input_seqs": ["NNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "NNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATCATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "NNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "naive_seq": "NNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGKV3-15*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ1*01": 1.0}, "v_3p_del": 6, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 276, "j": 303}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTCAACATC-1_contig_2"], "invalid": false, "v_gene": "IGKV3-11*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 30, "mature_cdr3_lengths": [30], "mut_freqs": [0.0219435736677116], "n_mutations": [7], "input_seqs": ["NNNNNNNNNNNNNNNGAAATTGTGTTGACACAATCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTTCTTAGCCTGGTATCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTCTGATACATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCATCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTCGCAACTGGCCCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "naive_seq": "NNNNNNNNNNNNNNNGAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV3-11*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 0.9999981868643554, "IGKJ1*01": 1.813135641141175e-06}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 276, "j": 303}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCAATGTAAG-1_contig_2"], "invalid": false, "v_gene": "IGKV2D-28*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 30, "mature_cdr3_lengths": [30], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "naive_seq": "GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV2D-28*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ1*01": 1.0}, "v_3p_del": 7, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 276, "j": 303}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCATCGTCGG-1_contig_2"], "invalid": false, "v_gene": "IGKV1D-39*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 30, "mature_cdr3_lengths": [30], "mut_freqs": [0.025078369905956112], "n_mutations": [8], "input_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAACTTTTTACATTGGTATCAGCAAAAACCAGGGAAAGCCCCTAACCTCCTGATCTATGCTGCATCCAGCTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTATGCAACTTACTACTGTCAACAGACTTACAGTACCCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "naive_seq": "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV1D-39*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 0.9999999556825837, "IGKJ3*01": 4.4317418443606924e-08}, "v_3p_del": 5, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 276, "j": 303}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/igk.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/igk.fa new file mode 100644 index 000000000..4a6e83d6a --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/igk.fa @@ -0,0 +1,42 @@ +>AAACCTGAGAGACGAA-1_contig_1 +GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCGGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCACAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>AAACCTGAGCGCCTTG-1_contig_1 +GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATATAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAATCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCGTTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC +>AAACCTGCAGAGCCAA-1_contig_1 +GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGGGCATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGCTTAATAGTTACCCGATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC +>AAACCTGCAGGGTTAG-1_contig_1 +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCCCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC +>AAACCTGCATCGACGC-1_contig_2 +GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCCCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCACTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>AAACCTGCATTACCTT-1_contig_1 +GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAACAGCTTCTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCGTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACTGACTTCACGCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGGAGTTTATTACTGTCAGCAACGTAGCAACTGGCCTCAGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>AAACCTGGTCTTGCGG-1_contig_1 +GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>AAACCTGGTGAACCTT-1_contig_1 +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCGAGTCAGGGCATTAGCAATTATTTAGCCTGGTATCAGCAGAAACCAGGGAAAGTTCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAATCAGGGGTCCCATCTCGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATGTTGCAACTTATTACTGTCAAAAGTATAACAGTGCCCCGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>AAACCTGGTTACGCGC-1_contig_2 +GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCTTCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>AAACCTGTCATATCGG-1_contig_2 +GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCTCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>AAACCTGTCGGAAACG-1_contig_1 +GACATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGGGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCGGCTATTTACATTGGTATCAGCAGAAACCAGGGAAAGCCCCTGAATTCCTGATTTATCTTGCATCCAGTTTGCAAAGTGGGGTCCCATCTAGGTTCCGTGGCAGTGGATCTGGGACATATTTCACTCTCACCATCAGCAGTCTTCAGGTTGAAGATTTTGCGACTTACTACTGTCAACAGAGTTACAGTACCCCTCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>AAACGGGAGAAACGCC-1_contig_2 +GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTTTATAGTGATGGAGACACCTACTTGAATTGGTTTCACCAGAGGCCAGGCCAATCTCCAAGGCGCCTATTTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACATACTGGCCTTACACTCTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>AAACGGGAGCGTTGCC-1_contig_1 +GATATTGTGATGACCCAGACTCCACTCTCCTCACCTGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTACACAGTGATGGAAACACCTACTTGAGTTGGCTTCAGCAGAGGCCAGGCCAGCCTCCAAGACTCCTAATTTATAAGATTTCTAACCGGTTCTCTGGGGTCCCAGACAGATTCAGTGGCAGTGGGGCAGGGACAGATTTCACACTGAAAATCAGCAGGGTGGAAGCTGAGGATGTCGGGGTTTATTACTGCATGCAAGCTACACAATTTCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>AAACGGGAGTCATCCA-1_contig_2 +GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>AAACGGGGTTGTACAC-1_contig_1 +GCCATCCAGTTGACCCAGTCTCCATCCTCCCTCTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGCTGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCACCAGTTTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAATTTAACAGTTACCTCCACACTTTCGGCCCTGGGACCAAAGTGGAAATCAAAC +>AAACGGGTCGTGACAT-1_contig_1 +GCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAGAACCAGGGAAAGCCCCTAACCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCGGACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>AAAGATGAGCTGAACG-1_contig_1 +GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC +>AAAGATGAGGACCACA-1_contig_1 +GACATCCAGATGACCCAGTCTCCGTCTTCCGTGTCTGCATCTGTGGGAGACAGAGTCACCATCATTTGTCGGGCGAGTCACGGTATCAGCAGGATGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCCGCAGACACCTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGAGCTGGGACAGAATTCTCTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC +>AAAGATGCAATGTAAG-1_contig_1 +GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>AAAGATGCACCAGCAC-1_contig_2 +GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCTATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC +>AAAGATGGTATAATGG-1_contig_2 +GAAATTGTGCTGACTCAGTCTCCAGACTTTCAGTCTGTGACTCCAAAGGAGAAAGTCACCATCACCTGCCGGGCCAGTCAGAGCATTGGTAGTAGCTTACACTGGTACCAGCAGAAACCAGATCAGTCTCCAAAGCTCCTCATCAAGTATGCTTCCCAGTCCTTCTCAGGGGTCCCCTCGAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACCCTCACCATCAATAGCCTGGAAGCTGAAGATGCTGCAACGTATTACTGTCATCAGAGTAGTAGTTTCCCTTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/igl.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/igl.fa new file mode 100644 index 000000000..67bc0cf87 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/igl.fa @@ -0,0 +1,12 @@ +>AAACCTGTCATCGCTC-1_contig_2 +TCCTATGACCTGACTCAGCCACCCTCCGTGTCCGTGTCCCCAGGCCAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGAGATAAATTTGTTTCCTGGTATGAACAGAGGCCAGGCCAGTCCCCTGTCCTGGTCATCTATCAAGATAGGAAGTGGCCCTCAGGGATCCCTGATCGATTCTCTGGCTCCAAGTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCAATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGTAGTAGTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>AAACCTGTCTGGCGAC-1_contig_2 +CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGGGCCTTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>AAACGGGAGGTAGCTG-1_contig_1 +TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>AAACGGGTCCGTTGTC-1_contig_1 +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCCTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>AAAGATGAGGCGCTCT-1_contig_2 +TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGCGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>AAAGATGCAGCGTCCA-1_contig_2 +TCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCGCAGGAGATATACTGGCAAAAAGATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTATTGGTGATTTATAAAGACACTGAGCGGCCCTCAGGGATCCCTGAGCGAATCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATAGAGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/partition-igk.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/partition-igk.yaml new file mode 100644 index 000000000..a880ff239 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/partition-igk.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-12*01": "GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTCC", "IGKV1-27*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCGAGTCAGGGCATTAGCAATTATTTAGCCTGGTATCAGCAGAAACCAGGGAAAGTTCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAATCAGGGGTCCCATCTCGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATGTTGCAACTTATTACTGTCAAAAGTATAACAGTGCCCCTCC", "IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1-5*01": "GACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGAGTATTAGTAGCTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAGTATAATAGTTATTCTCC", "IGKV1-8*03": "GCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCTCC", "IGKV1-9*01": "GACATCCAGTTGACCCAGTCTCCATCCTTCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGGGCATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGCTTAATAGTTACCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV1D-39*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCC", "IGKV2-24*01": "GATATTGTGATGACCCAGACTCCACTCTCCTCACCTGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTACACAGTGATGGAAACACCTACTTGAGTTGGCTTCAGCAGAGGCCAGGCCAGCCTCCAAGACTCCTAATTTATAAGATTTCTAACCGGTTCTCTGGGGTCCCAGACAGATTCAGTGGCAGTGGGGCAGGGACAGATTTCACACTGAAAATCAGCAGGGTGGAAGCTGAGGATGTCGGGGTTTATTACTGCATGCAAGCTACACAATTTCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV2D-28*01": "GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC", "IGKV3-20*01": "GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTCC", "IGKV4-1*02": "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCCTCC", "IGKV6-21*01": "GAAATTGTGCTGACTCAGTCTCCAGACTTTCAGTCTGTGACTCCAAAGGAGAAAGTCACCATCACCTGCCGGGCCAGTCAGAGCATTGGTAGTAGCTTACACTGGTACCAGCAGAAACCAGATCAGTCTCCAAAGCTCCTCATCAAGTATGCTTCCCAGTCCTTCTCAGGGGTCCCCTCGAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACCCTCACCATCAATAGCCTGGAAGCTGAAGATGCTGCAACGTATTACTGTCATCAGAGTAGTAGTTTACCTCA"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*03": "TGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*04": "TGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-5*01": 261, "IGKV1-9*01": 261, "IGKV3-20*01": 264, "IGKV2-24*01": 276, "IGKV1-33*01": 261, "IGKV1-12*01": 261, "IGKV2D-28*01": 276, "IGKV1-27*01": 261, "IGKV6-21*01": 261, "IGKV3-11*01": 261, "IGKV1D-39*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV4-1*02": 279, "IGKV2-30*01": 276, "IGKV1-8*03": 261}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*04": 8, "IGKJ2*03": 8, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": -1757.3681439746338, "n_clusters": 20, "n_procs": 1, "partition": [["AAACCTGAGAGACGAA-1_contig_1"], ["AAACCTGAGCGCCTTG-1_contig_1"], ["AAACCTGCAGAGCCAA-1_contig_1"], ["AAACCTGCAGGGTTAG-1_contig_1"], ["AAACCTGCATCGACGC-1_contig_2"], ["AAACCTGCATTACCTT-1_contig_1"], ["AAACCTGGTCTTGCGG-1_contig_1"], ["AAACCTGGTGAACCTT-1_contig_1"], ["AAACCTGGTTACGCGC-1_contig_2"], ["AAACCTGTCATATCGG-1_contig_2", "AAACGGGAGTCATCCA-1_contig_2"], ["AAACCTGTCGGAAACG-1_contig_1"], ["AAACGGGAGAAACGCC-1_contig_2"], ["AAACGGGAGCGTTGCC-1_contig_1"], ["AAACGGGGTTGTACAC-1_contig_1"], ["AAACGGGTCGTGACAT-1_contig_1"], ["AAAGATGAGCTGAACG-1_contig_1"], ["AAAGATGAGGACCACA-1_contig_1"], ["AAAGATGCAATGTAAG-1_contig_1"], ["AAAGATGCACCAGCAC-1_contig_2"], ["AAAGATGGTATAATGG-1_contig_2"]]}, {"logprob": -1721.4534563263614, "n_clusters": 19, "n_procs": 1, "partition": [["AAACCTGAGAGACGAA-1_contig_1"], ["AAACCTGAGCGCCTTG-1_contig_1"], ["AAACCTGCAGAGCCAA-1_contig_1"], ["AAACCTGCAGGGTTAG-1_contig_1"], ["AAACCTGCATCGACGC-1_contig_2"], ["AAACCTGCATTACCTT-1_contig_1"], ["AAACCTGGTCTTGCGG-1_contig_1"], ["AAACCTGGTGAACCTT-1_contig_1"], ["AAACCTGGTTACGCGC-1_contig_2"], ["AAACCTGTCATATCGG-1_contig_2", "AAACGGGAGTCATCCA-1_contig_2"], ["AAACCTGTCGGAAACG-1_contig_1"], ["AAACGGGAGAAACGCC-1_contig_2", "AAAGATGCAATGTAAG-1_contig_1"], ["AAACGGGAGCGTTGCC-1_contig_1"], ["AAACGGGGTTGTACAC-1_contig_1"], ["AAACGGGTCGTGACAT-1_contig_1"], ["AAAGATGAGCTGAACG-1_contig_1"], ["AAAGATGAGGACCACA-1_contig_1"], ["AAAGATGCACCAGCAC-1_contig_2"], ["AAAGATGGTATAATGG-1_contig_2"]]}], "events": [{"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["AAACCTGTCATATCGG-1_contig_2", "AAACGGGAGTCATCCA-1_contig_2"], "invalid": false, "v_gene": "IGKV2D-28*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33], "mut_freqs": [0.002967359050445104, 0.0], "n_mutations": [1, 0], "input_seqs": ["NNNGATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCTCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "NNNGATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "naive_seq": "NNNGATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGKV2D-28*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 1.0, "IGKJ3*01": 6.073947765423925e-19}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 279, "j": 309}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["AAACGGGAGAAACGCC-1_contig_2", "AAAGATGCAATGTAAG-1_contig_1"], "invalid": false, "v_gene": "IGKV2-30*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ2*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33], "mut_freqs": [0.02373887240356083, 0.0], "n_mutations": [8, 0], "input_seqs": ["NNNGATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTTTATAGTGATGGAGACACCTACTTGAATTGGTTTCACCAGAGGCCAGGCCAATCTCCAAGGCGCCTATTTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACATACTGGCCTTACACTCTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "NNNGATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC"], "naive_seq": "NNNGATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGKV2-30*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ2*01": 0.9998458978885671, "IGKJ2*03": 0.00015410211143900972}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [true, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 279, "j": 309}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGAGAGACGAA-1_contig_1"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.006211180124223602], "n_mutations": [2], "input_seqs": ["NNNNNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCGGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCACAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "naive_seq": "NNNNNNNNNNNNNNNNNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV3-15*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 0.9999999994816022, "IGKJ3*01": 5.183994662411653e-10}, "v_3p_del": 2, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 279, "j": 309}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGAGCGCCTTG-1_contig_1"], "invalid": false, "v_gene": "IGKV2-30*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ3*01", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.005934718100890208], "n_mutations": [2], "input_seqs": 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"", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 279, "j": 309}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/partition-igl.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/partition-igl.yaml new file mode 100644 index 000000000..0bd0e48ad --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-33/partition-igl.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV1-51*02": "CAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCAGGAACAGCCCCCAAACTCCTCATCTATGAAAATAATAAGCGACCCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGGAACATGGGATAGCAGCCTGAGTGCTGG", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC", "IGLV3-1*01": "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGCA", "IGLV3-19*01": "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATCT", "IGLV3-27*01": "TCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCTCAGGAGATGTACTGGCAAAAAAATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTGCTGGTGATTTATAAAGACAGTGAGCGGCCCTCAGGGATCCCTGAGCGATTCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATCT", "IGLV4-60*03": "CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTAGCTACATCATCGCATGGCATCAGCAGCAGCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAGGTAGTGGAAGCTACAACAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGGGCTGACCGCTACCTCACCATCTCCAACCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCA", "IGLV7-46*04": "CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGG", "IGLV8-61*01": "CAGACTGTGGTGACCCAGGAGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTTACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGGCTCCACGCACGCTCATCTACAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGAACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTACTGTGTGCTGTATATGGGTAGTGGCATTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"}}, "cyst-positions": {"IGLV8-61*01": 267, "IGLV2-14*04": 267, "IGLV4-60*03": 273, "IGLV2-23*02": 267, "IGLV1-40*01": 267, "IGLV3-1*01": 258, "IGLV1-51*02": 264, "IGLV7-46*04": 267, "IGLV3-27*01": 258, "IGLV3-19*01": 258}, "phen-positions": {"IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": -505.27396243114714, "n_clusters": 6, "n_procs": 1, "partition": [["AAACCTGTCATCGCTC-1_contig_2"], ["AAACCTGTCTGGCGAC-1_contig_2"], ["AAACGGGAGGTAGCTG-1_contig_1"], ["AAACGGGTCCGTTGTC-1_contig_1"], ["AAAGATGAGGCGCTCT-1_contig_2"], ["AAAGATGCAGCGTCCA-1_contig_2"]]}, {"logprob": -466.98714934557813, "n_clusters": 5, "n_procs": 1, "partition": [["AAACCTGTCATCGCTC-1_contig_2", "AAAGATGAGGCGCTCT-1_contig_2"], ["AAACCTGTCTGGCGAC-1_contig_2"], ["AAACGGGAGGTAGCTG-1_contig_1"], ["AAACGGGTCCGTTGTC-1_contig_1"], ["AAAGATGCAGCGTCCA-1_contig_2"]]}, {"logprob": -437.13643260011406, "n_clusters": 4, "n_procs": 1, "partition": [["AAACCTGTCATCGCTC-1_contig_2", "AAAGATGAGGCGCTCT-1_contig_2", "AAACGGGAGGTAGCTG-1_contig_1"], ["AAACCTGTCTGGCGAC-1_contig_2"], ["AAACGGGTCCGTTGTC-1_contig_1"], ["AAAGATGCAGCGTCCA-1_contig_2"]]}], "events": [{"has_shm_indels": [false, false, false], "qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["AAACCTGTCATCGCTC-1_contig_2", "AAAGATGAGGCGCTCT-1_contig_2", "AAACGGGAGGTAGCTG-1_contig_1"], "invalid": false, "v_gene": "IGLV3-1*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33], "mut_freqs": [0.05956112852664577, 0.003134796238244514, 0.006269592476489028], "n_mutations": [19, 1, 2], "input_seqs": ["NNNNNNNNNTCCTATGACCTGACTCAGCCACCCTCCGTGTCCGTGTCCCCAGGCCAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGAGATAAATTTGTTTCCTGGTATGAACAGAGGCCAGGCCAGTCCCCTGTCCTGGTCATCTATCAAGATAGGAAGTGGCCCTCAGGGATCCCTGATCGATTCTCTGGCTCCAAGTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCAATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGTAGTAGTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "NNNNNNNNNTCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGCGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "NNNNNNNNNTCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "NNNNNNNNNTCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGLV3-1*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ2*01": 0.9908931334814428, "IGLJ3*02": 0.009106866518562785}, "v_3p_del": 5, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "C", "fv_insertion": "NNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 267, "j": 297}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCTGGCGAC-1_contig_2"], "invalid": false, "v_gene": "IGLV7-46*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGGGCCTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGGGCCTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV7-46*04": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.5161803483489827, "IGLJ2*01": 0.4838196516510166}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GCC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 297}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGTCCGTTGTC-1_contig_1"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCCTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCCTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV2-23*02": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ1*01": 1.0}, "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 297}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCAGCGTCCA-1_contig_2"], "invalid": false, "v_gene": "IGLV3-27*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.025078369905956112], "n_mutations": [8], "input_seqs": ["NNNNNNNNNTCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCGCAGGAGATATACTGGCAAAAAGATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTATTGGTGATTTATAAAGACACTGAGCGGCCCTCAGGGATCCCTGAGCGAATCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATAGAGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "NNNNNNNNNTCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCTCAGGAGATGTACTGGCAAAAAAATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTGCTGGTGATTTATAAAGACAGTGAGCGGCCCTCAGGGATCCCTGAGCGATTCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV3-27*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.98680698577856, "IGLJ2*01": 0.013193014221439352}, "v_3p_del": 2, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "NNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 297}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/igh.fa new file mode 100644 index 000000000..f7b8a9256 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/igh.fa @@ -0,0 +1,2 @@ +>AAAGATGCACGGACAA-1_contig_2 +CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGAGGAAAATGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/igk.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/igk.fa new file mode 100644 index 000000000..3f851f1dc --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/igk.fa @@ -0,0 +1,14 @@ +>AAACCTGAGTGAACAT-1_contig_1 +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTGGGAGACAGAGTCACCATCACTTGCCGGGCAGGTCAGAACATTGGCAGCTATTTAAATTGGTATCAACAGAAGGCAGGGAAAGCCCCTAAACTCCTGATCTCTGCTGCATCGCATCTGCAGAGTGGGGTCCCATCACGGTTCAGTGGCAGTGGGTCTGGGACAGATTTCGCTCTCACCATCAGCAGTGTGCAACGTGAAGATTTTGCAACTTATTATTGTCAACAGAGTTACAGTACCCCTCCGTATAGTTTTGGCCAGGGGACCAAACTAGAGATCAAAC +>AAACCTGCAGTGAGTG-1_contig_2 +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGGTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>AAACCTGTCATCTGCC-1_contig_1 +GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCTTCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>AAACCTGTCCGGCACA-1_contig_1 +GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCCCCGATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC +>AAACGGGAGCACACAG-1_contig_1 +GCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCTCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>AAAGATGCACGACGAA-1_contig_1 +GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTCCGGGCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>AAAGATGCACGGACAA-1_contig_1 +GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCCGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/igl.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/igl.fa new file mode 100644 index 000000000..2b6baf694 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/igl.fa @@ -0,0 +1,6 @@ +>AAACGGGAGGGAGTAA-1_contig_1 +CAGACTGTGGTGACCCAGGTGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTCACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGACTCCACGCACGCTCATCTATAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGGACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTATTGTTTGCTATATATGCGTAGTGGCGTTTGGGTGTTCGGCGGAGGGACCAGGCTGACCGTCCTAG +>AAACGGGCATGACATC-1_contig_1 +CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTGGTTACTTGATCGCGTGGCATCAGCAGCACCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAAGTAGTGGAATCTACACCAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGCACTGACCGCTACCTCTCCATCTCCAATCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCCTGTGGTCTTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>AAAGATGCACGGACAA-1_contig_3 +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGCGTTATAATCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCACTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/partition-igh.yaml new file mode 100644 index 000000000..a122b29a9 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -38.87532348426752, "n_clusters": 1, "n_procs": 1, "partition": [["AAAGATGCACGGACAA-1_contig_2"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCACGGACAA-1_contig_2"], "invalid": false, "v_gene": "IGHV4-31*03", "d_gene": "IGHD1-1*01", "j_gene": "IGHJ3*02", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGAGGAAAATGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGAGGAAAATGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-31*03": 1.0}, "d_per_gene_support": {"IGHD1-1*01": 0.36441620754047893, "IGHD1-14*01": 0.22906198452970422, "IGHD1-7*01": 0.20492327519278372, "IGHD1-20*01": 0.1911932395003912, "IGHD3-3*01": 0.010405293236645737}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 4, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "AA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 321}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/partition-igk.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/partition-igk.yaml new file mode 100644 index 000000000..2da76a2d5 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/partition-igk.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-12*01": "GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTCC", "IGKV1-27*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCGAGTCAGGGCATTAGCAATTATTTAGCCTGGTATCAGCAGAAACCAGGGAAAGTTCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAATCAGGGGTCCCATCTCGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATGTTGCAACTTATTACTGTCAAAAGTATAACAGTGCCCCTCC", "IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1-5*01": "GACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGAGTATTAGTAGCTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAGTATAATAGTTATTCTCC", "IGKV1-8*03": "GCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCTCC", "IGKV1-9*01": "GACATCCAGTTGACCCAGTCTCCATCCTTCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGGGCATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGCTTAATAGTTACCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV1D-39*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCC", "IGKV2-24*01": "GATATTGTGATGACCCAGACTCCACTCTCCTCACCTGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTACACAGTGATGGAAACACCTACTTGAGTTGGCTTCAGCAGAGGCCAGGCCAGCCTCCAAGACTCCTAATTTATAAGATTTCTAACCGGTTCTCTGGGGTCCCAGACAGATTCAGTGGCAGTGGGGCAGGGACAGATTTCACACTGAAAATCAGCAGGGTGGAAGCTGAGGATGTCGGGGTTTATTACTGCATGCAAGCTACACAATTTCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV2D-28*01": "GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC", "IGKV3-20*01": "GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTCC", "IGKV4-1*02": "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCCTCC", "IGKV6-21*01": "GAAATTGTGCTGACTCAGTCTCCAGACTTTCAGTCTGTGACTCCAAAGGAGAAAGTCACCATCACCTGCCGGGCCAGTCAGAGCATTGGTAGTAGCTTACACTGGTACCAGCAGAAACCAGATCAGTCTCCAAAGCTCCTCATCAAGTATGCTTCCCAGTCCTTCTCAGGGGTCCCCTCGAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACCCTCACCATCAATAGCCTGGAAGCTGAAGATGCTGCAACGTATTACTGTCATCAGAGTAGTAGTTTACCTCA"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*03": "TGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*04": "TGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-5*01": 261, "IGKV1-9*01": 261, "IGKV3-20*01": 264, "IGKV2-24*01": 276, "IGKV1-33*01": 261, "IGKV1-12*01": 261, "IGKV2D-28*01": 276, "IGKV1-27*01": 261, "IGKV6-21*01": 261, "IGKV3-11*01": 261, "IGKV1D-39*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV4-1*02": 279, "IGKV2-30*01": 276, "IGKV1-8*03": 261}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*04": 8, "IGKJ2*03": 8, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": -552.4554065459923, "n_clusters": 7, "n_procs": 1, "partition": [["AAACCTGAGTGAACAT-1_contig_1"], ["AAACCTGCAGTGAGTG-1_contig_2"], ["AAACCTGTCATCTGCC-1_contig_1"], ["AAACCTGTCCGGCACA-1_contig_1"], ["AAACGGGAGCACACAG-1_contig_1"], ["AAAGATGCACGACGAA-1_contig_1"], ["AAAGATGCACGGACAA-1_contig_1"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGAGTGAACAT-1_contig_1"], "invalid": false, "v_gene": "IGKV1D-39*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ2*03", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.07384615384615385], "n_mutations": [24], "input_seqs": 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"v_per_gene_support": {"IGKV3-11*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 1.0}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 264, "j": 297}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCCGGCACA-1_contig_1"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ5*01", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.003076923076923077], "n_mutations": [1], "input_seqs": 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"fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 264, "j": 297}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGCACACAG-1_contig_1"], "invalid": false, "v_gene": "IGKV1-8*03", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ2*01", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNGCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCTCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC"], "naive_seq": "NNNGCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCTCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV1-8*03": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ2*01": 0.9942198458315546, "IGKJ2*03": 0.00578015416844679}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 264, "j": 297}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCACGACGAA-1_contig_1"], "invalid": false, "v_gene": "IGKV3-20*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTCCGGGCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "naive_seq": "GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTCCGGGCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV3-20*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 0.9999999704909546, "IGKJ1*01": 2.950904443689047e-08}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 264, "j": 297}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCACGGACAA-1_contig_1"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCCGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "naive_seq": "NNNGAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCCGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV3-15*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ1*01": 1.0}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 264, "j": 297}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/partition-igl.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/partition-igl.yaml new file mode 100644 index 000000000..762ca93a9 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-36/partition-igl.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV1-51*02": "CAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCAGGAACAGCCCCCAAACTCCTCATCTATGAAAATAATAAGCGACCCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGGAACATGGGATAGCAGCCTGAGTGCTGG", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC", "IGLV3-1*01": "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGCA", "IGLV3-19*01": "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATCT", "IGLV3-27*01": "TCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCTCAGGAGATGTACTGGCAAAAAAATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTGCTGGTGATTTATAAAGACAGTGAGCGGCCCTCAGGGATCCCTGAGCGATTCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATCT", "IGLV4-60*03": "CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTAGCTACATCATCGCATGGCATCAGCAGCAGCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAGGTAGTGGAAGCTACAACAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGGGCTGACCGCTACCTCACCATCTCCAACCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCA", "IGLV7-46*04": "CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGG", "IGLV8-61*01": "CAGACTGTGGTGACCCAGGAGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTTACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGGCTCCACGCACGCTCATCTACAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGAACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTACTGTGTGCTGTATATGGGTAGTGGCATTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"}}, "cyst-positions": {"IGLV8-61*01": 267, "IGLV2-14*04": 267, "IGLV4-60*03": 273, "IGLV2-23*02": 267, "IGLV1-40*01": 267, "IGLV3-1*01": 258, "IGLV1-51*02": 264, "IGLV7-46*04": 267, "IGLV3-27*01": 258, "IGLV3-19*01": 258}, "phen-positions": {"IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": -346.80023466249287, "n_clusters": 3, "n_procs": 1, "partition": [["AAACGGGAGGGAGTAA-1_contig_1"], ["AAACGGGCATGACATC-1_contig_1"], ["AAAGATGCACGGACAA-1_contig_3"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGGGAGTAA-1_contig_1"], "invalid": false, "v_gene": "IGLV8-61*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.03323262839879154], "n_mutations": [11], "input_seqs": ["NNNNNNCAGACTGTGGTGACCCAGGTGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTCACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGACTCCACGCACGCTCATCTATAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGGACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTATTGTTTGCTATATATGCGTAGTGGCGTTTGGGTGTTCGGCGGAGGGACCAGGCTGACCGTCCTAG"], "naive_seq": "NNNNNNCAGACTGTGGTGACCCAGGAGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTTACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGGCTCCACGCACGCTCATCTACAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGAACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTACTGTGTGCTGTATATGGGTAGTGGCATTTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV8-61*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.9112556727062637, "IGLJ2*01": 0.08874432729372951}, "v_3p_del": 2, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 273, "j": 306}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGCATGACATC-1_contig_1"], "invalid": false, "v_gene": "IGLV4-60*03", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.04154302670623145], "n_mutations": [14], "input_seqs": ["CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTGGTTACTTGATCGCGTGGCATCAGCAGCACCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAAGTAGTGGAATCTACACCAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGCACTGACCGCTACCTCTCCATCTCCAATCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCCTGTGGTCTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTAGCTACATCATCGCATGGCATCAGCAGCAGCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAGGTAGTGGAAGCTACAACAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGGGCTGACCGCTACCTCACCATCTCCAACCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCCTGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV4-60*03": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ2*01": 0.9953572783978399, "IGLJ3*02": 0.00464272160216174}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 273, "j": 306}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCACGGACAA-1_contig_3"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 36, "mature_cdr3_lengths": [36], "mut_freqs": [0.00906344410876133], "n_mutations": [3], "input_seqs": ["NNNNNNCAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGCGTTATAATCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCACTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "NNNNNNCAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV2-23*02": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.9784972680425973, "IGLJ2*01": 0.021502731957398286}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 273, "j": 306}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/igh.fa new file mode 100644 index 000000000..186c93c57 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/igh.fa @@ -0,0 +1,4 @@ +>AAACCTGAGCGCCTTG-1_contig_2 +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTACCTATGATATGCACTGGGTCCGCCAGGCTCCAGGCGAGGGGCTGGAATGGGTGGCAGTTATATCCTATGATGGAAGTAATAAATACCACGCAGACTCCGTGAAGGGCCGATTCATCATCTCCAGAGACAATTCCAGGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGTTTCGACTACCATAGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG +>AAACGGGTCCGTTGTC-1_contig_2 +CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGGGCAACTGGGGATCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/igk.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/igk.fa new file mode 100644 index 000000000..b949bbacc --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/igk.fa @@ -0,0 +1,6 @@ +>AAACCTGGTTCAGTAC-1_contig_1 +GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCCGATGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>AAACCTGTCCGAAGAG-1_contig_1 +GACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGGATATTAATAAGTGGTTGGCCTGGTATCGCCGGAGACCAGGGACAGCCCCTAACCTCCTGATCTATGATGCCTCCACTTTGGAAAATGGGGTCCCATCAAGGTTCAGCGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAATATAATAATTATATTCCCCCGCTCACTTTCGGCGGAGGGACCAAGGTTGAGATCAAAC +>AAAGATGAGACTAAGT-1_contig_1 +GCCTTCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCGTCTGAGGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGCCATTAGTCGTACTTTAGCCTGGTATCAGCAGAAACCAGGGAAAATTCCTGAACTCCTGATCTCTTATGGCTCCAATTTGGAAAGTGGGGTCCCATCTAGGTTCAGCGGCCATGTATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCGGCCTGGGGATTTTGCAACTTATTTCTGTCAACACTTTAATACTTTCACTCACGAAGTCACTTTCGGCGGAGGGACCAAGGTGGAGATTAAAC diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/igl.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/igl.fa new file mode 100644 index 000000000..7fca589ff --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/igl.fa @@ -0,0 +1,12 @@ +>AAACCTGCAAATACAG-1_contig_2 +CAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCACGAACAGCCCCCAAACTCCTCATTTACGAAAATAGTGAGCGATTCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGAAACATGGGATGACAGCCTGAGTGCTGGGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>AAACCTGCATCTACGA-1_contig_2 +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAACACCCAGGCAAAGCCCCCAAACTCGTTATTTATGATGTCAGTAGTCGGCCCTCAGGGGTCTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCGGGGTGTTCGGCGGAGGGACCAAGGTGACCGTCCTAG +>AAACCTGTCCGGCACA-1_contig_4 +CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>AAACGGGAGATCCGAG-1_contig_2 +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTAGGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>AAACGGGAGATCCGAG-1_contig_3 +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCGAGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>AAACGGGGTACAAGTA-1_contig_1 +TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igh.yaml new file mode 100644 index 000000000..52dcde319 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -144.7738917866887, "n_clusters": 2, "n_procs": 1, "partition": [["AAACCTGAGCGCCTTG-1_contig_2"], ["AAACGGGTCCGTTGTC-1_contig_2"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGAGCGCCTTG-1_contig_2"], "invalid": false, "v_gene": "IGHV3-30*04", "d_gene": "IGHD4-17*01", "j_gene": "IGHJ3*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.022535211267605635], "n_mutations": [8], "input_seqs": ["NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTACCTATGATATGCACTGGGTCCGCCAGGCTCCAGGCGAGGGGCTGGAATGGGTGGCAGTTATATCCTATGATGGAAGTAATAAATACCACGCAGACTCCGTGAAGGGCCGATTCATCATCTCCAGAGACAATTCCAGGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGTTTCGACTACCATAGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGTTTCGACTACCATAGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-30*04": 0.9999998897034378, "IGHV3-33*01": 1.1029655873674258e-07}, "d_per_gene_support": {"IGHD4-17*01": 0.7578913626706082, "IGHD3-22*01": 0.17837481780053802, "IGHD1-7*01": 0.02994394261997817, "IGHD1-26*01": 0.02754615755973515, "IGHD3-9*01": 0.006243719349139227}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 3, "d_5p_del": 10, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTTC", "dj_insertion": "CATAG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGTCCGTTGTC-1_contig_2"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD7-27*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGGGCAACTGGGGATCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGGGCAACTGGGGATCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD7-27*01": 0.9995072138925739, "IGHD1-20*01": 0.00013780569013004058, "IGHD1-1*01": 0.00013400815420798297, "IGHD6-13*01": 0.0001124738387770488, "IGHD1-7*01": 0.00010849842431122407}, "j_per_gene_support": {"IGHJ4*02": 0.9999988503513109, "IGHJ5*02": 1.149648689502121e-06}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGGC", "dj_insertion": "TC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igk.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igk.yaml new file mode 100644 index 000000000..43bed25a8 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igk.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-12*01": "GACATCCAGATGACCCAGTCTCCATCTTCCGTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGCTGGTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTACTATTGTCAACAGGCTAACAGTTTCCCTCC", "IGKV1-27*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCGAGTCAGGGCATTAGCAATTATTTAGCCTGGTATCAGCAGAAACCAGGGAAAGTTCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAATCAGGGGTCCCATCTCGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATGTTGCAACTTATTACTGTCAAAAGTATAACAGTGCCCCTCC", "IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1-5*01": "GACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGAGTATTAGTAGCTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAGTATAATAGTTATTCTCC", "IGKV1-8*03": "GCCATCCGGATGACCCAGTCTCCATCCTCACTCTCTGCATCTACAGGAGACAGAGTCACCATCACTTGTCGGGCGAGTCAGGGTATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCTGCCTGCAGTCTGAAGATTTTGCAACTTATTACTGTCAACAGTATTATAGTTACCCTCC", "IGKV1-9*01": "GACATCCAGTTGACCCAGTCTCCATCCTTCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGGGCATTAGCAGTTATTTAGCCTGGTATCAGCAAAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCACTTTGCAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGCTTAATAGTTACCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV1D-39*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGAGCATTAGCAGCTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCCATCAAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGTCTGCAACCTGAAGATTTTGCAACTTACTACTGTCAACAGAGTTACAGTACCCCTCC", "IGKV2-24*01": "GATATTGTGATGACCCAGACTCCACTCTCCTCACCTGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTACACAGTGATGGAAACACCTACTTGAGTTGGCTTCAGCAGAGGCCAGGCCAGCCTCCAAGACTCCTAATTTATAAGATTTCTAACCGGTTCTCTGGGGTCCCAGACAGATTCAGTGGCAGTGGGGCAGGGACAGATTTCACACTGAAAATCAGCAGGGTGGAAGCTGAGGATGTCGGGGTTTATTACTGCATGCAAGCTACACAATTTCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV2D-28*01": "GATATTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCCTGGAGAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGAGCCTCCTGCATAGTAATGGATACAACTATTTGGATTGGTACCTGCAGAAGCCAGGGCAGTCTCCACAGCTCCTGATCTATTTGGGTTCTAATCGGGCCTCCGGGGTCCCTGACAGGTTCAGTGGCAGTGGATCAGGCACAGATTTTACACTGAAAATCAGCAGAGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGCTCTACAAACTCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC", "IGKV3-20*01": "GAAATTGTGTTGACGCAGTCTCCAGGCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAGCTACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCAGCAGGGCCACTGGCATCCCAGACAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGACTGGAGCCTGAAGATTTTGCAGTGTATTACTGTCAGCAGTATGGTAGCTCACCTCC", "IGKV4-1*02": "GACATCGTGATGACCCAGTCTCCAGACTCCCTGGCTGTGTCTCTGGGCGAGAGGGCCACCATCAACTGCAAGTCCAGCCAGAGTGTTTTATACAGCTCCAACAATAAGAACTACTTAGCTTGGTACCAGCAGAAACCAGGACAGCCTCCTAAGCTGCTCATTTACTGGGCATCTACCCGGGAATCCGGGGTCCCTGACCGATTCAGTGGCAGCGGGTCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGGCTGAAGATGTGGCAGTTTATTACTGTCAGCAGTATTATAGTACTCCTCC", "IGKV6-21*01": "GAAATTGTGCTGACTCAGTCTCCAGACTTTCAGTCTGTGACTCCAAAGGAGAAAGTCACCATCACCTGCCGGGCCAGTCAGAGCATTGGTAGTAGCTTACACTGGTACCAGCAGAAACCAGATCAGTCTCCAAAGCTCCTCATCAAGTATGCTTCCCAGTCCTTCTCAGGGGTCCCCTCGAGGTTCAGTGGCAGTGGATCTGGGACAGATTTCACCCTCACCATCAATAGCCTGGAAGCTGAAGATGCTGCAACGTATTACTGTCATCAGAGTAGTAGTTTACCTCA"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*03": "TGTACAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ2*04": "TGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-5*01": 261, "IGKV1-9*01": 261, "IGKV3-20*01": 264, "IGKV2-24*01": 276, "IGKV1-33*01": 261, "IGKV1-12*01": 261, "IGKV2D-28*01": 276, "IGKV1-27*01": 261, "IGKV6-21*01": 261, "IGKV3-11*01": 261, "IGKV1D-39*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV4-1*02": 279, "IGKV2-30*01": 276, "IGKV1-8*03": 261}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*04": 8, "IGKJ2*03": 8, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": -585.4113163400667, "n_clusters": 3, "n_procs": 1, "partition": [["AAACCTGGTTCAGTAC-1_contig_1"], ["AAACCTGTCCGAAGAG-1_contig_1"], ["AAAGATGAGACTAAGT-1_contig_1"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTTCAGTAC-1_contig_1"], "invalid": false, "v_gene": "IGKV3-11*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ2*04", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCCGATGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC"], "naive_seq": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCCGATGTGCAGTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV3-11*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ2*04": 0.9800329739004993, "IGKJ2*03": 0.01996702609950291}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 261, "j": 297}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCCGAAGAG-1_contig_1"], "invalid": false, "v_gene": "IGKV1-5*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.06097560975609756], "n_mutations": [20], "input_seqs": ["GACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGGATATTAATAAGTGGTTGGCCTGGTATCGCCGGAGACCAGGGACAGCCCCTAACCTCCTGATCTATGATGCCTCCACTTTGGAAAATGGGGTCCCATCAAGGTTCAGCGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAATATAATAATTATATTCCCCCGCTCACTTTCGGCGGAGGGACCAAGGTTGAGATCAAAC"], "naive_seq": "GACATCCAGATGACCCAGTCTCCTTCCACCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCCAGTCAGAGTATTAGTAGCTGGTTGGCCTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGAATTCACTCTCACCATCAGCAGCCTGCAGCCTGATGATTTTGCAACTTATTACTGCCAACAGTATAATAGTTATTCTCCCCCGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV1-5*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 1.0}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CCC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 261, "j": 297}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGAGACTAAGT-1_contig_1"], "invalid": false, "v_gene": "IGKV1D-13*02", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.0975609756097561], "n_mutations": [32], "input_seqs": ["GCCTTCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCGTCTGAGGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGCCATTAGTCGTACTTTAGCCTGGTATCAGCAGAAACCAGGGAAAATTCCTGAACTCCTGATCTCTTATGGCTCCAATTTGGAAAGTGGGGTCCCATCTAGGTTCAGCGGCCATGTATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCGGCCTGGGGATTTTGCAACTTATTTCTGTCAACACTTTAATACTTTCACTCACGAAGTCACTTTCGGCGGAGGGACCAAGGTGGAGATTAAAC"], "naive_seq": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCACGGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGKV1D-13*02": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 0.9999972063310821, "IGKJ3*01": 2.7936689402730085e-06}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 261, "j": 297}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igl.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igl.yaml new file mode 100644 index 000000000..a0137b965 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igl.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV1-51*02": "CAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCAGGAACAGCCCCCAAACTCCTCATCTATGAAAATAATAAGCGACCCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGGAACATGGGATAGCAGCCTGAGTGCTGG", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC", "IGLV3-1*01": "TCCTATGAGCTGACTCAGCCACCCTCAGTGTCCGTGTCCCCAGGACAGACAGCCAGCATCACCTGCTCTGGAGATAAATTGGGGGATAAATATGCTTGCTGGTATCAGCAGAAGCCAGGCCAGTCCCCTGTGCTGGTCATCTATCAAGATAGCAAGCGGCCCTCAGGGATCCCTGAGCGATTCTCTGGCTCCAACTCTGGGAACACAGCCACTCTGACCATCAGCGGGACCCAGGCTATGGATGAGGCTGACTATTACTGTCAGGCGTGGGACAGCAGCACTGCA", "IGLV3-19*01": "TCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATCT", "IGLV3-27*01": "TCCTATGAGCTGACACAGCCATCCTCAGTGTCAGTGTCTCCGGGACAGACAGCCAGGATCACCTGCTCAGGAGATGTACTGGCAAAAAAATATGCTCGGTGGTTCCAGCAGAAGCCAGGCCAGGCCCCTGTGCTGGTGATTTATAAAGACAGTGAGCGGCCCTCAGGGATCCCTGAGCGATTCTCCGGCTCCAGCTCAGGGACCACAGTCACCTTGACCATCAGCGGGGCCCAGGTTGAGGATGAGGCTGACTATTACTGTTACTCTGCGGCTGACAACAATCT", "IGLV4-60*03": "CAGCCTGTGCTGACTCAATCATCCTCTGCCTCTGCTTCCCTGGGATCCTCGGTCAAGCTCACCTGCACTCTGAGCAGTGGGCACAGTAGCTACATCATCGCATGGCATCAGCAGCAGCCAGGGAAGGCCCCTCGGTACTTGATGAAGCTTGAAGGTAGTGGAAGCTACAACAAGGGGAGCGGAGTTCCTGATCGCTTCTCAGGCTCCAGCTCTGGGGCTGACCGCTACCTCACCATCTCCAACCTCCAGTCTGAGGATGAGGCTGATTATTACTGTGAGACCTGGGACAGTAACACTCA", "IGLV7-46*04": "CAGGCTGTGGTGACTCAGGAGCCCTCACTGACTGTGTCCCCAGGAGGGACAGTCACTCTCACCTGTGGCTCCAGCACTGGAGCTGTCACCAGTGGTCATTATCCCTACTGGTTCCAGCAGAAGCCTGGCCAAGCCCCCAGGACACTGATTTATGATACAAGCAACAAACACTCCTGGACCCCTGCCCGGTTCTCAGGCTCCCTCCTTGGGGGCAAAGCTGCCCTGACCCTTTCGGGTGCGCAGCCTGAGGATGAGGCTGAGTATTACTGCTTGCTCTCCTATAGTGGTGCTCGG", "IGLV8-61*01": "CAGACTGTGGTGACCCAGGAGCCATCGTTCTCAGTGTCCCCTGGAGGGACAGTCACACTCACTTGTGGCTTGAGCTCTGGCTCAGTCTCTACTAGTTACTACCCCAGCTGGTACCAGCAGACCCCAGGCCAGGCTCCACGCACGCTCATCTACAGCACAAACACTCGCTCTTCTGGGGTCCCTGATCGCTTCTCTGGCTCCATCCTTGGGAACAAAGCTGCCCTCACCATCACGGGGGCCCAGGCAGATGATGAATCTGATTATTACTGTGTGCTGTATATGGGTAGTGGCATTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ2*01": "TGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"}}, "cyst-positions": {"IGLV8-61*01": 267, "IGLV2-14*04": 267, "IGLV4-60*03": 273, "IGLV2-23*02": 267, "IGLV1-40*01": 267, "IGLV3-1*01": 258, "IGLV1-51*02": 264, "IGLV7-46*04": 267, "IGLV3-27*01": 258, "IGLV3-19*01": 258}, "phen-positions": {"IGLJ1*01": 7, "IGLJ2*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": -353.28785006285665, "n_clusters": 6, "n_procs": 1, "partition": [["AAACCTGCAAATACAG-1_contig_2"], ["AAACCTGCATCTACGA-1_contig_2"], ["AAACCTGTCCGGCACA-1_contig_4"], ["AAACGGGAGATCCGAG-1_contig_2"], ["AAACGGGAGATCCGAG-1_contig_3"], ["AAACGGGGTACAAGTA-1_contig_1"]]}, {"logprob": -328.8754231133806, "n_clusters": 5, "n_procs": 1, "partition": [["AAACCTGCAAATACAG-1_contig_2"], ["AAACCTGCATCTACGA-1_contig_2", "AAACGGGAGATCCGAG-1_contig_2"], ["AAACCTGTCCGGCACA-1_contig_4"], ["AAACGGGAGATCCGAG-1_contig_3"], ["AAACGGGGTACAAGTA-1_contig_1"]]}, {"logprob": -325.3869039181007, "n_clusters": 4, "n_procs": 1, "partition": [["AAACCTGCAAATACAG-1_contig_2"], ["AAACCTGCATCTACGA-1_contig_2", "AAACGGGAGATCCGAG-1_contig_2", "AAACGGGAGATCCGAG-1_contig_3"], ["AAACCTGTCCGGCACA-1_contig_4"], ["AAACGGGGTACAAGTA-1_contig_1"]]}], "events": [{"has_shm_indels": [false, false, false], "qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["AAACCTGCATCTACGA-1_contig_2", "AAACGGGAGATCCGAG-1_contig_2", "AAACGGGAGATCCGAG-1_contig_3"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39, 39], "mut_freqs": [0.017964071856287425, 0.0029940119760479044, 0.005988023952095809], "n_mutations": [6, 1, 2], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAACACCCAGGCAAAGCCCCCAAACTCGTTATTTATGATGTCAGTAGTCGGCCCTCAGGGGTCTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCGGGGTGTTCGGCGGAGGGACCAAGGTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTAGGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCGAGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCGGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGLV2-14*04": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 0.9971097965694344, "IGLJ2*01": 0.002890203430572608}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "G", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 267, "j": 303}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCAAATACAG-1_contig_2"], "invalid": false, "v_gene": "IGLV1-51*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.030211480362537766], "n_mutations": [10], "input_seqs": ["NNNCAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCACGAACAGCCCCCAAACTCCTCATTTACGAAAATAGTGAGCGATTCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGAAACATGGGATGACAGCCTGAGTGCTGGGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "NNNCAGTCTGTGTTGACGCAGCCGCCCTCAGTGTCTGCGGCCCCAGGACAGAAGGTCACCATCTCCTGCTCTGGAAGCAGCTCCAACATTGGGAATAATTATGTATCCTGGTACCAGCAGCTCCCAGGAACAGCCCCCAAACTCCTCATCTATGAAAATAATAAGCGACCCTCAGGGATTCCTGACCGATTCTCTGGCTCCAAGTCTGGCACGTCAGCCACCCTGGGCATCACCGGACTCCAGACTGGGGACGAGGCCGATTATTACTGCGGAACATGGGATAGCAGCCTGAGTGCTGGGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV1-51*02": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ2*01": 0.978075111167959, "IGLJ3*02": 0.02192488883204208}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 303}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCCGGCACA-1_contig_4"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV1-40*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ1*01": 1.0}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 303}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGGTACAAGTA-1_contig_1"], "invalid": false, "v_gene": "IGLV3-19*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ2*01", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNNNNTCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "NNNNNNNNNTCTTCTGAGCTGACTCAGGACCCTGCTGTGTCTGTGGCCTTGGGACAGACAGTCAGGATCACATGCCAAGGAGACAGCCTCAGAAGCTATTATGCAAGCTGGTACCAGCAGAAGCCAGGACAGGCCCCTGTACTTGTCATCTATGGTAAAAACAACCGGCCCTCAGGGATCCCAGACCGATTCTCTGGCTCCAGCTCAGGAAACACAGCTTCCTTGACCATCACTGGGGCTCAGGCGGAAGATGAGGCTGACTATTACTGTAACTCCCGGGACAGCAGTGGTAACCATGTGGTATTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGLV3-19*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ2*01": 0.9999737961760137, "IGLJ3*02": 2.620382398641891e-05}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 267, "j": 303}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-42/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-42/igh.fa new file mode 100644 index 000000000..5b478afbc --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-42/igh.fa @@ -0,0 +1,2 @@ +>AAACGGGAGGCCCTTG-1_contig_1 +CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGTTTATCGGAAGAGCCGACTCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-42/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-42/partition-igh.yaml new file mode 100644 index 000000000..56a05d9d4 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-42/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -61.890104824884354, "n_clusters": 1, "n_procs": 1, "partition": [["AAACGGGAGGCCCTTG-1_contig_1"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGGCCCTTG-1_contig_1"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD3-16*03", "j_gene": "IGHJ4*02", "cdr3_length": 42, "mature_cdr3_lengths": [42], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGTTTATCGGAAGAGCCGACTCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGTTTATCGGAAGAGCCGACTCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD3-16*03": 0.9310442101738194, "IGHD1-14*01": 0.04633032725224545, "IGHD2-15*01": 0.014955419805124543, "IGHD1-20*01": 0.007234185405310662, "IGHD1-1*01": 0.00043585736350145}, "j_per_gene_support": {"IGHJ4*02": 0.9999998924315165, "IGHJ5*02": 1.0756848660121791e-07}, "v_3p_del": 3, "d_5p_del": 24, "d_3p_del": 7, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "T", "dj_insertion": "GAAGAGCCGACTCCT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 324}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-45/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-45/igh.fa new file mode 100644 index 000000000..faca7a64f --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-45/igh.fa @@ -0,0 +1,12 @@ +>AAACCTGCATTACCTT-1_contig_2 +CAGTTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCCTCTGGAGGCACCCTCAACAGCCTTGCTATCAACTGGCTACGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGGTCATCCCTATCCTTGGTTCAGGAAACTACGCACAGAAGTTTCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAACACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTCTATTACTGTGCGAGAGAGCTAGGACTGGGTCACTGGAATTACCTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACCTGGTAACGCGA-1_contig_1 +GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGATCTAGGTAGGCTGGATGGTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACCTGGTGAACCTT-1_contig_2 +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGGAGCTACGGTGACTACGCCCCTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACCTGTCCGGCACA-1_contig_2 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGTACCCGGCGTATAGCAGCACCCATTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAAGATGAGCTGAACG-1_contig_2 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGTCGTAGAGTGGGACAAAGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG +>AAAGATGCAATGTAAG-1_contig_4 +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGATTGGGCTAACTGGGGCGACCTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-45/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-45/partition-igh.yaml new file mode 100644 index 000000000..73266a1e8 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-45/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -425.07157197607097, "n_clusters": 6, "n_procs": 1, "partition": [["AAACCTGCATTACCTT-1_contig_2"], ["AAACCTGGTAACGCGA-1_contig_1"], ["AAACCTGGTGAACCTT-1_contig_2"], ["AAACCTGTCCGGCACA-1_contig_2"], ["AAAGATGAGCTGAACG-1_contig_2"], ["AAAGATGCAATGTAAG-1_contig_4"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCATTACCTT-1_contig_2"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD1-7*01", "j_gene": "IGHJ4*02", "cdr3_length": 45, "mature_cdr3_lengths": [45], "mut_freqs": [0.05263157894736842], "n_mutations": [19], "input_seqs": ["CAGTTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCCTCTGGAGGCACCCTCAACAGCCTTGCTATCAACTGGCTACGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGGTCATCCCTATCCTTGGTTCAGGAAACTACGCACAGAAGTTTCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAACACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTCTATTACTGTGCGAGAGAGCTAGGACTGGGTCACTGGAATTACCTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGAGCTAGGACTGGGTAACTGGAACTACCTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD1-7*01": 0.9502658519350609, "IGHD5-24*01": 0.035687118223285366, "IGHD1-20*01": 0.010957243994994387, "IGHD1-1*01": 0.0025742617386916118, "IGHD3-9*01": 0.0005155241079793496}, "j_per_gene_support": {"IGHJ4*02": 0.9999974143576257, "IGHJ5*02": 2.5856423601643623e-06}, "v_3p_del": 0, "d_5p_del": 4, "d_3p_del": 0, "j_5p_del": 10, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GCTAGGACTGGG", "dj_insertion": "CT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 327}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTAACGCGA-1_contig_1"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 45, "mature_cdr3_lengths": [45], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGATCTAGGTAGGCTGGATGGTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGATCTAGGTAGGCTGGATGGTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-23*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.7478217279004046, "IGHD6-13*01": 0.17741553169676633, "IGHD1-7*01": 0.040215625650895016, "IGHD1-20*01": 0.03445081373326357, "IGHD1-1*01": 9.630101867286223e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999999986251353, "IGHJ5*02": 1.3748667750774514e-09}, "v_3p_del": 0, "d_5p_del": 12, "d_3p_del": 3, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCTAGGTA", "dj_insertion": "ATGGT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 327}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTGAACCTT-1_contig_2"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD4-17*01", "j_gene": "IGHJ4*02", "cdr3_length": 45, "mature_cdr3_lengths": [45], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGGAGCTACGGTGACTACGCCCCTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGGAGCTACGGTGACTACGCCCCTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD4-17*01": 0.9999926157828297, "IGHD1-26*01": 4.971463053350522e-06, "IGHD1-7*01": 2.367132184516755e-06, "IGHD2-15*01": 4.481766871826698e-08, "IGHD2-21*01": 8.042657357595704e-10}, "j_per_gene_support": {"IGHJ4*02": 0.99999999856675, "IGHJ5*02": 1.4332474813617514e-09}, "v_3p_del": 3, "d_5p_del": 3, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GAG", "dj_insertion": "GCCCCT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 327}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCCGGCACA-1_contig_2"], "invalid": false, "v_gene": "IGHV1-46*03", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 45, "mature_cdr3_lengths": [45], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGTACCCGGCGTATAGCAGCACCCATTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGTACCCGGCGTATAGCAGCACCCATTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-46*03": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9356149093348343, "IGHD6-6*01": 0.04148798927009923, "IGHD6-19*01": 0.021481067593892768, "IGHD1-26*01": 0.0014091532191198195, "IGHD1-14*01": 6.8805820534008124e-06}, "j_per_gene_support": {"IGHJ4*02": 0.9999999260156357, "IGHJ5*02": 7.398436321440364e-08}, "v_3p_del": 3, "d_5p_del": 2, "d_3p_del": 8, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TACCCGGC", "dj_insertion": "CCCATT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 327}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGAGCTGAACG-1_contig_2"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ3*02", "cdr3_length": 45, "mature_cdr3_lengths": [45], "mut_freqs": [0.002770083102493075], "n_mutations": [1], "input_seqs": ["CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGTCGTAGAGTGGGACAAAGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "naive_seq": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGTCGTATAGTGGGACAAAGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD1-26*01": 0.9970192959445057, "IGHD3-3*01": 0.001777423997654941, "IGHD5-24*01": 0.0008211209367145209, "IGHD6-19*01": 0.00038193880626976505, "IGHD1-1*01": 2.203148548753439e-07}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 8, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "CAAA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 327}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCAATGTAAG-1_contig_4"], "invalid": false, "v_gene": "IGHV3-11*01", "d_gene": "IGHD7-27*01", "j_gene": "IGHJ4*02", "cdr3_length": 45, "mature_cdr3_lengths": [45], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGATTGGGCTAACTGGGGCGACCTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGATTGGGCTAACTGGGGCGACCTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-11*01": 1.0}, "d_per_gene_support": {"IGHD7-27*01": 0.9891473212381491, "IGHD1-20*01": 0.009149518732152835, "IGHD1-7*01": 0.001477743526882303, "IGHD3-16*03": 0.0001924057761416745, "IGHD1-1*01": 3.301072667172665e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999999822266049, "IGHJ5*02": 1.7773397540160055e-08}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 1, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTGGG", "dj_insertion": "CGACCT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 327}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-48/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-48/igh.fa new file mode 100644 index 000000000..d20597484 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-48/igh.fa @@ -0,0 +1,12 @@ +>AAACCTGCAAATACAG-1_contig_1 +GAGGTGCAGCTGGTGGAATCTGGGGGAGGCTTGGTCCAGCGGGGGGGGTCCCTGAGACTCTCCTGCGCAGCCTCTGGATTCACCTTTACTAAATGTTGCATGAGTTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACGTTAAGCCAGATGGAAGTGAGAAATGCTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAGCTTACTGTATCTGCAAATGAACAGCCTGAGAGTCGAGGACACGGCTGTATATTACTGTGCGACAGTTAGGGGCCCTAGTGGACGAGGACCTCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACCTGTCGGAAACG-1_contig_2 +GAATTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTGCAGCCTGGCGGGTCCCTGAGACTCACCTGTGTAGTCTCTGGATTCACGTTTGATGACTTTGGCATGCACTGGGTCCGGCAAACTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTCGTTGGGATAGTAGTAACATAGACTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGACCTCAGGACACGGGCATATATTATTGTGCAAGAGCTTTTGAAGCCAAAGTCAAAGATGCTTTTAATCTCTGGGGCCACGGAACAATGGTCTCCGTCTCCTCAG +>AAACGGGAGATAGCAT-1_contig_1 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGTACGGATGGTATCAGCTGGGTGCGACAGGCCCCTGGAGAAAGGCTTGAGTGGATGGGAGGAATCATCCCTGTCTTTGGTAGAGCAAACAACGCACAGAAGTTCCAGGGCAGACTCACGATTAGCGCGGACGAGTCCACGACAACAGTGTACATGGAATTGAGCAGCCTGAGATCTGAGGACACGGCCATCTATTACTGTGCGAGGCTTAGAGTGGGGTCTAGGAAAAATTGGTTCGACCCCTGGGGCCAGGGAACCCAGGTCACCGTCTCCTCAG +>AAAGATGAGACTAAGT-1_contig_2 +CGGCTGCAACTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACATGCAATGTCTCTGGTGGCTCCATCAGCAGTATTGCTGACTACTGGGTCTGGATCCGCCAGCCCCCCGGGAAGGGACTGGAATGGATTGGGACTCTGTCGTATAGTTGGACCACCTCCTACACCGCGTCTCTCAAGAGTCGAGTCATCATTTCCGGAGATACGTCCAAGAACCAGGTCTCCCTGCAGGTGACCTCTGTGACCGCCGCAGACACGGCTGTGTATTATTGTGTGAAGCATTTGGGTAATTACTATGGTGCGGGGAGTTACGTCTGGGGCCACGGGACCACGGTCACCGTCTCCTCAG +>AAAGATGCACGACGAA-1_contig_2 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGCCGGCGTATTACTATGGTTCGGGGCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAAGATGCAGCGTCCA-1_contig_1 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGTTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTACTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGGTGACGCTGATTCGGGGAATTATCTTGGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-48/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-48/partition-igh.yaml new file mode 100644 index 000000000..acffc0eb5 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-48/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -1145.7444004846166, "n_clusters": 6, "n_procs": 1, "partition": [["AAACCTGCAAATACAG-1_contig_1"], ["AAACCTGTCGGAAACG-1_contig_2"], ["AAACGGGAGATAGCAT-1_contig_1"], ["AAAGATGAGACTAAGT-1_contig_2"], ["AAAGATGCACGACGAA-1_contig_2"], ["AAAGATGCAGCGTCCA-1_contig_1"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCAAATACAG-1_contig_1"], "invalid": false, "v_gene": "IGHV3-7*01", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.057692307692307696], "n_mutations": [21], "input_seqs": ["NNNGAGGTGCAGCTGGTGGAATCTGGGGGAGGCTTGGTCCAGCGGGGGGGGTCCCTGAGACTCTCCTGCGCAGCCTCTGGATTCACCTTTACTAAATGTTGCATGAGTTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACGTTAAGCCAGATGGAAGTGAGAAATGCTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAGCTTACTGTATCTGCAAATGAACAGCCTGAGAGTCGAGGACACGGCTGTATATTACTGTGCGACAGTTAGGGGCCCTAGTGGACGAGGACCTCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGTTCGGGGCCCTAGTGGACGAGGACCTCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-7*01": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 0.5068629860733477, "IGHD1-26*01": 0.3924517982353347, "IGHD3-22*01": 0.05322257894869435, "IGHD6-19*01": 0.029798370852487176, "IGHD2-15*01": 0.017664265890114137}, "j_per_gene_support": {"IGHJ4*02": 0.9999999501308435, "IGHJ5*02": 4.986916057124858e-08}, "v_3p_del": 1, "d_5p_del": 12, "d_3p_del": 12, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CCCTAGTGGACGAGGACCTCC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCGGAAACG-1_contig_2"], "invalid": false, "v_gene": "IGHV3-9*01", "d_gene": "IGHD3-9*01", "j_gene": "IGHJ3*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.10989010989010989], "n_mutations": [40], "input_seqs": ["NNNGAATTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTGCAGCCTGGCGGGTCCCTGAGACTCACCTGTGTAGTCTCTGGATTCACGTTTGATGACTTTGGCATGCACTGGGTCCGGCAAACTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTCGTTGGGATAGTAGTAACATAGACTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGACCTCAGGACACGGGCATATATTATTGTGCAAGAGCTTTTGAAGCCAAAGTCAAAGATGCTTTTAATCTCTGGGGCCACGGAACAATGGTCTCCGTCTCCTCAG"], "naive_seq": "NNNGAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGCTTTTGACTGGTTATTATAACATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-9*01": 1.0}, "d_per_gene_support": {"IGHD3-9*01": 0.5834827432622784, "IGHD3-3*01": 0.32314976250141697, "IGHD3-16*03": 0.07095258781747935, "IGHD1-1*01": 0.01867115606737792, "IGHD2-15*01": 0.003743750351457934}, "j_per_gene_support": {"IGHJ3*02": 0.9999993151347226, "IGHJ5*02": 6.848652832146955e-07}, "v_3p_del": 3, "d_5p_del": 11, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "C", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGATAGCAT-1_contig_1"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.10164835164835165], "n_mutations": [37], "input_seqs": ["NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGTACGGATGGTATCAGCTGGGTGCGACAGGCCCCTGGAGAAAGGCTTGAGTGGATGGGAGGAATCATCCCTGTCTTTGGTAGAGCAAACAACGCACAGAAGTTCCAGGGCAGACTCACGATTAGCGCGGACGAGTCCACGACAACAGTGTACATGGAATTGAGCAGCCTGAGATCTGAGGACACGGCCATCTATTACTGTGCGAGGCTTAGAGTGGGGTCTAGGAAAAATTGGTTCGACCCCTGGGGCCAGGGAACCCAGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGCGTATAGTGGGAGCTACTACAAATTGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD1-26*01": 0.9889249504659002, "IGHD6-19*01": 0.00746585115923314, "IGHD6-13*01": 0.00149855819793677, "IGHD3-3*01": 0.001264320020534458, "IGHD5-24*01": 0.0008463201563881217}, "j_per_gene_support": {"IGHJ4*02": 0.500613749691736, "IGHJ5*02": 0.49938625030825123}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GC", "dj_insertion": "AAATTGG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGAGACTAAGT-1_contig_2"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD7-27*01", "j_gene": "IGHJ6*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.13896457765667575], "n_mutations": [51], "input_seqs": ["CGGCTGCAACTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACATGCAATGTCTCTGGTGGCTCCATCAGCAGTATTGCTGACTACTGGGTCTGGATCCGCCAGCCCCCCGGGAAGGGACTGGAATGGATTGGGACTCTGTCGTATAGTTGGACCACCTCCTACACCGCGTCTCTCAAGAGTCGAGTCATCATTTCCGGAGATACGTCCAAGAACCAGGTCTCCCTGCAGGTGACCTCTGTGACCGCCGCAGACACGGCTGTGTATTATTGTGTGAAGCATTTGGGTAATTACTATGGTGCGGGGAGTTACGTCTGGGGCCACGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACAACTGGGGAACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD7-27*01": 0.7784212219554767, "IGHD3-10*01": 0.09219489811568703, "IGHD3-16*03": 0.07085097971518625, "IGHD3-3*01": 0.04149221395367854, "IGHD1-26*01": 0.017040686259935895}, "j_per_gene_support": {"IGHJ6*02": 0.9781054984217379, "IGHJ4*02": 0.021894501578272992}, "v_3p_del": 0, "d_5p_del": 3, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCACGACGAA-1_contig_2"], "invalid": false, "v_gene": "IGHV3-66*01", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGCCGGCGTATTACTATGGTTCGGGGCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGCCGGCGTATTACTATGGTTCGGGGCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-66*01": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 0.9999895277899583, "IGHD3-22*01": 1.047221003997173e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999999855632994, "IGHJ5*02": 1.4436703566130662e-08}, "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 12, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGGC", "dj_insertion": "C", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCAGCGTCCA-1_contig_1"], "invalid": false, "v_gene": "IGHV3-48*02", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.01098901098901099], "n_mutations": [4], "input_seqs": ["NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGTTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTACTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGGTGACGCTGATTCGGGGAATTATCTTGGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGGTGACGCTGGTTCGGGGAGTTATCTTGGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-48*02": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 0.9997213334674824, "IGHD7-27*01": 0.0001278167826033714, "IGHD5-24*01": 0.00011808442710822162, "IGHD3-16*03": 3.0188101376738855e-05, "IGHD2-21*01": 2.5772214277408446e-06}, "j_per_gene_support": {"IGHJ4*02": 0.999991448386269, "IGHJ5*02": 8.551613737043554e-06}, "v_3p_del": 1, "d_5p_del": 9, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTGACGC", "dj_insertion": "CTTGGA", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 333}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-51/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-51/igh.fa new file mode 100644 index 000000000..b36bf6f77 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-51/igh.fa @@ -0,0 +1,16 @@ +>AAACCTGAGAGACGAA-1_contig_2 +GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGAGTCACCTTTAACAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGCTAACACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATTTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTATATTACTGTGCCGCTACCCTAGGGACCCGTAGAGATGGTTACAATTTTGCATACTGGGGCCAGGAAACCCTGGTCACCGTCTCCTCAG +>AAACCTGCAGTGAGTG-1_contig_1 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGATTGGGATTCTCCCCCACAATCTTTCAAAACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACCTGCATCGACGC-1_contig_1 +GAGGTGCAACTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACCGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTACTAATAGTGATGGGACTAGGACAAACTACGCGGACACCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTACAAGAGCCCGTGCGATTTTTTTTGACGGGGACGGTATGGACGTCTGGGGCCGAGGGACCACGGTCACCGTCTCCGCAG +>AAACCTGTCATCTGCC-1_contig_2 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATCTGGCGGGTATAGCAGCAGCTGGTACTAGTGGCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACGGGAGATCCGAG-1_contig_1 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGATCTAAGATTTTTGGAGTGGTTCAGCGAGGCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACGGGAGCACACAG-1_contig_2 +CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACTCACAAGGTATAACTGGACCGGAGGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG +>AAACGGGAGGGAGTAA-1_contig_2 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTGCCTGAGGCTCTCCTGTTCAGCCTCTGGATTCACCTTTAGTAACTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAACCAAGATGGGAGTGTCAATAACTATGTGGACTCTGTGAAGGGCCGATTCACCGTCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGTGAGAGCTCCCACGGTGACTACGAGGGTGCTGGGCGACTGGGGCCAGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACGGGAGGTAGCTG-1_contig_2 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATATCGAGGATGATAGTAGTGGTTATTATTTAAGCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-51/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-51/partition-igh.yaml new file mode 100644 index 000000000..b7d56af1a --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-51/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -813.8961746122719, "n_clusters": 8, "n_procs": 1, "partition": [["AAACCTGAGAGACGAA-1_contig_2"], ["AAACCTGCAGTGAGTG-1_contig_1"], ["AAACCTGCATCGACGC-1_contig_1"], ["AAACCTGTCATCTGCC-1_contig_2"], ["AAACGGGAGATCCGAG-1_contig_1"], ["AAACGGGAGCACACAG-1_contig_2"], ["AAACGGGAGGGAGTAA-1_contig_2"], ["AAACGGGAGGTAGCTG-1_contig_2"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGAGAGACGAA-1_contig_2"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD5-24*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mature_cdr3_lengths": [51], "mut_freqs": [0.027247956403269755], "n_mutations": [10], "input_seqs": ["NNNNNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGAGTCACCTTTAACAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGCTAACACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATTTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTATATTACTGTGCCGCTACCCTAGGGACCCGTAGAGATGGTTACAATTTTGCATACTGGGGCCAGGAAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCCGCTACCCTAGGGACCCGTAGAGATGGCTACAATTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-23*01": 1.0}, "d_per_gene_support": {"IGHD5-24*01": 0.9999988248443769, "IGHD3-10*01": 1.094263334304368e-06, "IGHD6-13*01": 7.637501865828803e-08, "IGHD2-15*01": 4.516998216316679e-09, "IGHD3-9*01": 2.8350881601936103e-13}, "j_per_gene_support": {"IGHJ4*02": 0.9999771975552739, "IGHJ5*02": 2.2802444731079653e-05}, "v_3p_del": 6, "d_5p_del": 0, "d_3p_del": 3, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CGCTACCCTAGGGACCC", "dj_insertion": "", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 339}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCAGTGAGTG-1_contig_1"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD5-24*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mature_cdr3_lengths": [51], "mut_freqs": [0.013623978201634877], "n_mutations": [5], "input_seqs": ["NNNNNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAGGGATCATCCCTATCTTTGGTACAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACGAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGATTGGGATTCTCCCCCACAATCTTTCAAAACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNCAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGATTGGGATTCTCCCCCACAATCTTTCAAAACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD5-24*01": 0.5209306885804192, "IGHD1-26*01": 0.27051755582019915, "IGHD3-3*01": 0.10577497894474475, "IGHD3-16*03": 0.10225758750003128, "IGHD3-9*01": 0.0005191891546178683}, "j_per_gene_support": {"IGHJ4*02": 0.9999999883842464, "IGHJ5*02": 1.1615760332427918e-08}, "v_3p_del": 2, "d_5p_del": 12, "d_3p_del": 3, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTGGGATTCTCCCCC", "dj_insertion": "CTTTCAAA", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 339}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCATCGACGC-1_contig_1"], "invalid": false, "v_gene": "IGHV3-74*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ6*02", "cdr3_length": 51, "mature_cdr3_lengths": [51], "mut_freqs": [0.02997275204359673], "n_mutations": [11], "input_seqs": ["NNNNNNGAGGTGCAACTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACCGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTACTAATAGTGATGGGACTAGGACAAACTACGCGGACACCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTACAAGAGCCCGTGCGATTTTTTTTGACGGGGACGGTATGGACGTCTGGGGCCGAGGGACCACGGTCACCGTCTCCGCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGCCCGTACGATTTTTTTTGACGGGGACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-74*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.8569912081418918, "IGHD3-10*01": 0.13836756512262954, "IGHD3-9*01": 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["NNNNNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATCTGGCGGGTATAGCAGCAGCTGGTACTAGTGGCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATCTGGCGGGTATAGCAGCAGCTGGTACTAGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999032059273802, "IGHD6-19*01": 9.679407262615431e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9997719051760254, "IGHJ5*02": 0.00022809482397529354}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCTGGC", "dj_insertion": "TAG", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 339}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGATCCGAG-1_contig_1"], "invalid": false, "v_gene": "IGHV3-15*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mature_cdr3_lengths": [51], "mut_freqs": [0.002680965147453083], "n_mutations": [1], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGATCTAAGATTTTTGGAGTGGTTCAGCGAGGCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGATCTACGATTTTTGGAGTGGTTCAGCGAGGCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-15*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9999998377453768, "IGHD3-9*01": 1.3305155366958874e-07, "IGHD3-10*01": 2.5507656823766486e-08, "IGHD3-22*01": 2.564090089346565e-09, "IGHD2-15*01": 1.1313217898866989e-09}, "j_per_gene_support": {"IGHJ4*02": 0.999998235333373, "IGHJ5*02": 1.7646666281250867e-06}, "v_3p_del": 0, "d_5p_del": 4, "d_3p_del": 8, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "CAGCGAGGC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 339}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGCACACAG-1_contig_2"], "invalid": false, "v_gene": "IGHV2-5*02", "d_gene": "IGHD1-20*01", "j_gene": "IGHJ1*01", "cdr3_length": 51, "mature_cdr3_lengths": [51], "mut_freqs": [0.002702702702702703], "n_mutations": [1], "input_seqs": ["NNNCAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACTCACAAGGTATAACTGGACCGGAGGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACTCACAAGGTATAACTGGAACGGAGGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-5*02": 1.0}, "d_per_gene_support": {"IGHD1-20*01": 0.8519775023563346, "IGHD1-7*01": 0.14550509756307806, "IGHD1-14*01": 0.0019017739734221092, "IGHD1-1*01": 0.0005711468744460373, "IGHD7-27*01": 4.447923271929814e-05}, "j_per_gene_support": {"IGHJ1*01": 1.0}, "v_3p_del": 4, "d_5p_del": 0, "d_3p_del": 2, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCACAA", "dj_insertion": "GAG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 339}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGGGAGTAA-1_contig_2"], "invalid": false, "v_gene": "IGHV3-7*01", "d_gene": "IGHD4-17*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mature_cdr3_lengths": [51], "mut_freqs": [0.04087193460490463], "n_mutations": [15], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTGCCTGAGGCTCTCCTGTTCAGCCTCTGGATTCACCTTTAGTAACTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAACCAAGATGGGAGTGTCAATAACTATGTGGACTCTGTGAAGGGCCGATTCACCGTCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGTGAGAGCTCCCACGGTGACTACGAGGGTGCTGGGCGACTGGGGCCAGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGCTCCCACGGTGACTACGAGGGTGCTGGGCGACTGGGGCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-7*01": 1.0}, "d_per_gene_support": {"IGHD4-17*01": 0.9998756058705934, "IGHD3-22*01": 8.940934045616106e-05, "IGHD3-10*01": 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["NNNNNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATATCGAGGATGATAGTAGTGGTTATTATTTAAGCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATATCGAGGATGATAGTAGTGGTTATTATTTAAGCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 0.9999974185861683, "IGHD3-3*01": 2.5805562501984406e-06, "IGHD2-15*01": 8.510335351139805e-10, "IGHD3-9*01": 6.464602558806074e-12, "IGHD2-21*01": 8.461823723158061e-14}, "j_per_gene_support": {"IGHJ4*02": 0.9997246177485456, "IGHJ5*02": 0.00027538225145328063}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 4, "j_5p_del": 10, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TATCGAGG", "dj_insertion": "TTTAAG", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 339}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-54/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-54/igh.fa new file mode 100644 index 000000000..0908fc35a --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-54/igh.fa @@ -0,0 +1,10 @@ +>AAACCTGGTTACGCGC-1_contig_1 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGCTTACTATGAACGTGGGTCGTGGAATAACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG +>AAACCTGTCATATCGG-1_contig_1 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACACCATATTACGATTTTTGGAGTGGTTATTTGGTCGGGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACCTGTCATCGCTC-1_contig_1 +CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAATACTAACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGATATATCTATTATAGTGGCAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAGGAACCAGTTCTCCCTGAAGCTGACCTCTGTGACCGCTGCGGACACGGCCCTGTATTACTGTGCGAGAGTCGAGGCTGATGGGGGTGGGCGCCCATACTACTTTGATTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAAGATGCACCAGCAC-1_contig_1 +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATATGGCTTTGGAACCACAACCGTCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG +>AAAGATGCATCGTCGG-1_contig_1 +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTGGCTATGCCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATTTGGTATGATGGAAGTAATAAATACTATACAGACTCCGTGGAGGGCCGATTCACCCTCTCCAGAGACAATTCCAAGAACACGATGTATCTGCAAATGAACAGCCTGAGAGTCGAGGACACGGCTGTGTATTACTGTGCGAGACCCCGAGAGCCGACGGCTGGTTCGGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAA diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-54/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-54/partition-igh.yaml new file mode 100644 index 000000000..7ecdcc410 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-54/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -483.38782338452825, "n_clusters": 5, "n_procs": 1, "partition": [["AAACCTGGTTACGCGC-1_contig_1"], ["AAACCTGTCATATCGG-1_contig_1"], ["AAACCTGTCATCGCTC-1_contig_1"], ["AAAGATGCACCAGCAC-1_contig_1"], ["AAAGATGCATCGTCGG-1_contig_1"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTTACGCGC-1_contig_1"], "invalid": false, "v_gene": "IGHV3-20*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ6*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGCTTACTATGAACGTGGGTCGTGGAATAACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGCTTACTATGAACGTGGGTCGTGGAATAACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-20*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 0.9618796117867076, "IGHD3-10*01": 0.03778968943551056, "IGHD3-16*03": 0.0003071869678910023, "IGHD1-20*01": 2.3224379748518177e-05, "IGHD1-1*01": 2.874301450932932e-07}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 1, "d_5p_del": 3, "d_3p_del": 19, "j_5p_del": 15, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "C", "dj_insertion": "ACGTGGGTCGTGGAATA", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 342}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCATATCGG-1_contig_1"], "invalid": false, "v_gene": "IGHV3-15*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACACCATATTACGATTTTTGGAGTGGTTATTTGGTCGGGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACACCATATTACGATTTTTGGAGTGGTTATTTGGTCGGGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-15*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9999997507863752, "IGHD3-9*01": 2.483983202437593e-07, "IGHD3-22*01": 8.153071119304453e-10}, "j_per_gene_support": {"IGHJ4*02": 0.999989619643965, "IGHJ5*02": 1.0380356038202481e-05}, "v_3p_del": 2, "d_5p_del": 1, "d_3p_del": 5, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCA", "dj_insertion": "TGGTCGGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 342}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCATCGCTC-1_contig_1"], "invalid": false, "v_gene": "IGHV4-59*11", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.035422343324250684], "n_mutations": [13], "input_seqs": ["NNNNNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAATACTAACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGATATATCTATTATAGTGGCAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAGGAACCAGTTCTCCCTGAAGCTGACCTCTGTGACCGCTGCGGACACGGCCCTGTATTACTGTGCGAGAGTCGAGGCTGATGGGGGTGGGCGCCCATACTACTTTGATTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGTCGAGGCTGATAGTAGTGGGCGCCCATACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-59*11": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 0.43144101882707037, "IGHD6-19*01": 0.35752482936206487, "IGHD1-26*01": 0.2038182799871515, "IGHD3-16*03": 0.004498359669719308, "IGHD2-21*01": 0.0027175121539647165}, "j_per_gene_support": {"IGHJ4*02": 0.9999999998951239, "IGHJ1*01": 1.0486576627145092e-10}, "v_3p_del": 1, "d_5p_del": 9, "d_3p_del": 10, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCGAGGC", "dj_insertion": "GCGCCCAT", "fv_insertion": "NNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 342}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCACCAGCAC-1_contig_1"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD1-14*01", "j_gene": "IGHJ6*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATATGGCTTTGGAACCACAACCGTCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATATGGCTTTGGAACCACAACCGTCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD1-14*01": 0.892999409954882, "IGHD1-7*01": 0.0748517072930181, "IGHD1-20*01": 0.029155685018106302, "IGHD3-3*01": 0.002618236292084178, "IGHD1-1*01": 0.00037496144191113333}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 13, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TATGGCTTT", "dj_insertion": "AACCGTC", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 342}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCATCGTCGG-1_contig_1"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ3*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.024324324324324326], "n_mutations": [9], "input_seqs": ["NNNNNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTGGCTATGCCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATTTGGTATGATGGAAGTAATAAATACTATACAGACTCCGTGGAGGGCCGATTCACCCTCTCCAGAGACAATTCCAAGAACACGATGTATCTGCAAATGAACAGCCTGAGAGTCGAGGACACGGCTGTGTATTACTGTGCGAGACCCCGAGAGCCGACGGCTGGTTCGGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAA"], "naive_seq": "NNNNNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGACCCCGAGAGCCGACGGCTGGTTCGGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 0.9999999922051188, "IGHV3-30*04": 7.794877827130093e-09}, "d_per_gene_support": {"IGHD3-10*01": 0.9055579984443902, "IGHD6-19*01": 0.08116290652199351, "IGHD6-13*01": 0.013118052389358202, "IGHD5-24*01": 0.0001606216509870141, "IGHD3-9*01": 4.209932854595402e-07}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 2, "d_5p_del": 9, "d_3p_del": 13, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCCGAGAGCCGACGGC", "dj_insertion": "", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 291, "j": 342}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-57/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-57/igh.fa new file mode 100644 index 000000000..66460999c --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-57/igh.fa @@ -0,0 +1,4 @@ +>AAACGGGCATGACATC-1_contig_2 +CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCATTGTCTCTGGTGGCCCCATCAGCAGTGGTAGTTACTCCTGGGGCTGGATCCGCCAGCCCCCACGGAAGGGGCTGGAGTGGCTTGGGGCTATCTATAATACTGGGAGATCTTACTACAACCCGTCTCTCAAGAGTCGCGTCACCATATCCGTAGACACGTCAAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCCGCAGACACGGCTATATATTACTGCGCGAGGTCAGAACGTATAGCAGTGGATCGTACCCCACGGGGCACGGAATATTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAAGATGCAATGTAAG-1_contig_3 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGACGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGACAGGGGGGCTACTCTGAAAACTATTCATTAAAGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-57/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-57/partition-igh.yaml new file mode 100644 index 000000000..240a7d63e --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-57/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -292.14006783819224, "n_clusters": 2, "n_procs": 1, "partition": [["AAACGGGCATGACATC-1_contig_2"], ["AAAGATGCAATGTAAG-1_contig_3"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGCATGACATC-1_contig_2"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.06382978723404255], "n_mutations": [24], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCATTGTCTCTGGTGGCCCCATCAGCAGTGGTAGTTACTCCTGGGGCTGGATCCGCCAGCCCCCACGGAAGGGGCTGGAGTGGCTTGGGGCTATCTATAATACTGGGAGATCTTACTACAACCCGTCTCTCAAGAGTCGCGTCACCATATCCGTAGACACGTCAAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCCGCAGACACGGCTATATATTACTGCGCGAGGTCAGAACGTATAGCAGTGGATCGTACCCCACGGGGCACGGAATATTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGGTCAGAACGTATAGCAGTGGCTGGTACCCCACGGGGCACGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9821070803271689, "IGHD6-13*01": 0.017516010449585572, "IGHD3-22*01": 0.0003697927170610881, "IGHD6-6*01": 6.983565650314765e-06, "IGHD2-15*01": 1.3294053240762605e-07}, "j_per_gene_support": {"IGHJ4*02": 0.9999997630828258, "IGHJ5*02": 2.369171732344157e-07}, "v_3p_del": 3, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTCAGAAC", "dj_insertion": "CCCACGGGGCACG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 342}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGCAATGTAAG-1_contig_3"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ2*01", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.005361930294906166], "n_mutations": [2], "input_seqs": ["NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGACGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGACAGGGGGGCTACTCTGAAAACTATTCATTAAAGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGACAGGGGAGCTACTCTGAAAACTATTCATTAAAGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD1-26*01": 0.8209763296529342, "IGHD3-22*01": 0.12742707980879137, "IGHD2-15*01": 0.03659216981066991, "IGHD5-24*01": 0.014986267442208, "IGHD2-21*01": 1.8153285378179455e-05}, "j_per_gene_support": {"IGHJ2*01": 1.0}, "v_3p_del": 2, "d_5p_del": 8, "d_3p_del": 2, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CAG", "dj_insertion": "CTGAAAACTATTCATTAAA", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 342}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-60/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-60/igh.fa new file mode 100644 index 000000000..36972e715 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-60/igh.fa @@ -0,0 +1,8 @@ +>AAACCTGCATCTACGA-1_contig_1 +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACCACATGAACTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTGGTAGTAGTGGTAGTACCATATATTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAAGGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGGGCTCCCCTTATTACTATGGTTCGGGGAGTTATTACAACTTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACCTGGTTCAGTAC-1_contig_2 +CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACCCTACTATGATAGTAGTGGTTATTACTTGACCGTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG +>AAAGATGAGGCGCTCT-1_contig_1 +CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGGGCTGTGGTGGTGATTGCTGGCGAGGACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG +>AAAGATGGTATAATGG-1_contig_1 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGACTTCTGGATACGCCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAATCCTAACAGTGGTGGCACAATCTATGCACAGGACTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAACTGAGCAGTCTGAGATCTGACGACACGGCCGTCTATTACTGTGCGAGAGCTTATTCCTATGATACTAGTGGTTATTCCTTGGTTCCCTATGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-60/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-60/partition-igh.yaml new file mode 100644 index 000000000..3559c049f --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-60/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -342.49722865507783, "n_clusters": 4, "n_procs": 1, "partition": [["AAACCTGCATCTACGA-1_contig_1"], ["AAACCTGGTTCAGTAC-1_contig_2"], ["AAAGATGAGGCGCTCT-1_contig_1"], ["AAAGATGGTATAATGG-1_contig_1"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCATCTACGA-1_contig_1"], "invalid": false, "v_gene": "IGHV3-11*01", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ4*02", "cdr3_length": 60, "mature_cdr3_lengths": [60], "mut_freqs": [0.015957446808510637], "n_mutations": [6], "input_seqs": ["NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACCACATGAACTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTGGTAGTAGTGGTAGTACCATATATTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAAGGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGGGCTCCCCTTATTACTATGGTTCGGGGAGTTATTACAACTTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGGGCTCCCCTTATTACTATGGTTCGGGGAGTTATTATAACTTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-11*01": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 1.0}, "j_per_gene_support": {"IGHJ4*02": 0.999999983627177, "IGHJ5*02": 1.6372822909218142e-08}, "v_3p_del": 5, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGCTCCCCT", "dj_insertion": "TT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 345}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTTCAGTAC-1_contig_2"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ3*02", "cdr3_length": 60, "mature_cdr3_lengths": [60], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACCCTACTATGATAGTAGTGGTTATTACTTGACCGTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACCCTACTATGATAGTAGTGGTTATTACTTGACCGTTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 1, "d_5p_del": 4, "d_3p_del": 2, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CC", "dj_insertion": "TGACCGT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 345}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGAGGCGCTCT-1_contig_1"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD2-21*01", "j_gene": "IGHJ6*02", "cdr3_length": 60, "mature_cdr3_lengths": [60], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGGGCTGTGGTGGTGATTGCTGGCGAGGACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGGGCTGTGGTGGTGATTGCTGGCGAGGACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-18*01": 1.0}, "d_per_gene_support": {"IGHD2-21*01": 0.9999757627804391, "IGHD2-15*01": 1.0712778919927556e-05, "IGHD3-22*01": 9.416602177096833e-06, "IGHD3-3*01": 4.104004976441703e-06, "IGHD3-9*01": 3.8334746047425575e-09}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 3, "d_5p_del": 7, "d_3p_del": 5, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGC", "dj_insertion": "GGCGAGG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 345}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGGTATAATGG-1_contig_1"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ4*02", "cdr3_length": 60, "mature_cdr3_lengths": [60], "mut_freqs": [0.03723404255319149], "n_mutations": [14], "input_seqs": ["NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGACTTCTGGATACGCCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAATCCTAACAGTGGTGGCACAATCTATGCACAGGACTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAACTGAGCAGTCTGAGATCTGACGACACGGCCGTCTATTACTGTGCGAGAGCTTATTCCTATGATACTAGTGGTTATTCCTTGGTTCCCTATGACTTCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGCTTATTACTATGATAGTAGTGGTTATTACTTGGTTCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ4*02": 0.9999988564592003, "IGHJ5*02": 1.1435408007416749e-06}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 2, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CT", "dj_insertion": "TGGTTCC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 345}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-63/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-63/igh.fa new file mode 100644 index 000000000..fdcc8354e --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-63/igh.fa @@ -0,0 +1,4 @@ +>AAACCTGGTCTTGCGG-1_contig_2 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGACGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGACGACCAGTTAACTGCATAGCAGCACGTCTATGTATTGGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG +>AAACGGGGTTGTACAC-1_contig_2 +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTGGAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCGGCGTCTGGATTCACCTTCAGTTACTATGGCATGCACTGGGTCCGCCGGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAATTATCTGGGATAATGGAAATGACAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGTTGTTTCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTTTGTATTACTGTGCGAGGCACCGAGGAAATTGTGGTGGTGGTACCTGCGTAGGGTCACGTCTGGACGTCTGGGGCCAGGGGACCACGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-63/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-63/partition-igh.yaml new file mode 100644 index 000000000..b4c9926af --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-63/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -270.8480124121909, "n_clusters": 2, "n_procs": 1, "partition": [["AAACCTGGTCTTGCGG-1_contig_2"], ["AAACGGGGTTGTACAC-1_contig_2"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTCTTGCGG-1_contig_2"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ3*02", "cdr3_length": 63, "mature_cdr3_lengths": [63], "mut_freqs": [0.010554089709762533], "n_mutations": [4], "input_seqs": ["CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGACGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGACGACCAGTTAACTGCATAGCAGCACGTCTATGTATTGGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "naive_seq": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGACGACCAGTTAACTGCATAGCAGCTCGTCCATGTATTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD6-6*01": 0.8369257634822812, "IGHD6-13*01": 0.16067109270932736, "IGHD6-19*01": 0.0020041326486766047, "IGHD7-27*01": 0.00037155787968004556, "IGHD1-20*01": 2.745328003210877e-05}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 2, "d_5p_del": 4, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CGACCAGTTAACTGC", "dj_insertion": "ATGTAT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 345}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGGTTGTACAC-1_contig_2"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD2-15*01", "j_gene": "IGHJ6*02", "cdr3_length": 63, "mature_cdr3_lengths": [63], "mut_freqs": [0.055408970976253295], "n_mutations": [21], "input_seqs": ["CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTGGAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCGGCGTCTGGATTCACCTTCAGTTACTATGGCATGCACTGGGTCCGCCGGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAATTATCTGGGATAATGGAAATGACAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGTTGTTTCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTTTGTATTACTGTGCGAGGCACCGAGGAAATTGTGGTGGTGGTACCTGCGTAGGGTCACGTCTGGACGTCTGGGGCCAGGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGGCACCGAGGATATTGTAGTGGTGGTAGCTGCGTAGGGTCACGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD2-15*01": 0.999963012960405, "IGHD2-21*01": 3.6987039601488806e-05}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 6, "j_5p_del": 18, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GCACCG", "dj_insertion": "GTAGGGTCAC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 345}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-66/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-66/igh.fa new file mode 100644 index 000000000..80a9178b4 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-66/igh.fa @@ -0,0 +1,8 @@ +>AAACCTGCAGAGCCAA-1_contig_2 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGATCTTCCAATACTATGCTATGGTTCGGGGAGTTATTCCCCGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG +>AAACCTGGTCAACATC-1_contig_1 +CAGGTGCAACTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGACATCTATCATAGTGGGAGCAGCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTTGACATGTCCAAGAACCAGTTGTCCCTGCACTTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGGTCCCCGGCGAACTATTACTATGCTTCGGGGTATCTACCCTCTTGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG +>AAACGGGAGTCATCCA-1_contig_1 +CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACACCGGGGGGAATTCGATTACTATGGTTCGGGGAGTTTCAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAACGGGGTACAAGTA-1_contig_2 +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATTGTTCAGGCGATTTTTGGAGTGGTTATTATCGATACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-66/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-66/partition-igh.yaml new file mode 100644 index 000000000..04ee0041f --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-66/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -354.708573307432, "n_clusters": 4, "n_procs": 1, "partition": [["AAACCTGCAGAGCCAA-1_contig_2"], ["AAACCTGGTCAACATC-1_contig_1"], ["AAACGGGAGTCATCCA-1_contig_1"], ["AAACGGGGTACAAGTA-1_contig_2"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCAGAGCCAA-1_contig_2"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ3*02", "cdr3_length": 66, "mature_cdr3_lengths": [66], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGATCTTCCAATACTATGCTATGGTTCGGGGAGTTATTCCCCGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGATCTTCCAATACTATGCTATGGTTCGGGGAGTTATTCCCCGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 0.9999999999985363, "IGHD3-16*03": 1.4659259871385777e-12}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 2, "d_5p_del": 6, "d_3p_del": 5, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCTTCCAATACTATG", "dj_insertion": "CCCC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 351}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGGTCAACATC-1_contig_1"], "invalid": false, "v_gene": "IGHV4-4*02", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ6*02", "cdr3_length": 66, "mature_cdr3_lengths": [66], "mut_freqs": [0.028795811518324606], "n_mutations": [11], "input_seqs": ["NNNCAGGTGCAACTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGACATCTATCATAGTGGGAGCAGCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTTGACATGTCCAAGAACCAGTTGTCCCTGCACTTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGGTCCCCGGCGAACTATTACTATGCTTCGGGGTATCTACCCTCTTGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGGTCCCCGGCGAACTATTACTATGGTTCGGGGTATCTACCCTCTTGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-4*02": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 0.9999868460063215, "IGHD3-22*01": 1.2977478135069948e-05, "IGHD3-3*01": 1.7547063077071915e-07, "IGHD6-13*01": 7.666435509412171e-10, "IGHD3-9*01": 2.782472096374846e-10}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 12, "j_5p_del": 18, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTCCCCGGCGAAC", "dj_insertion": "TATCTACCCTCTT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 351}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGTCATCCA-1_contig_1"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ5*02", "cdr3_length": 66, "mature_cdr3_lengths": [66], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACACCGGGGGGAATTCGATTACTATGGTTCGGGGAGTTTCAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACACCGGGGGGAATTCGATTACTATGGTTCGGGGAGTTTCAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD3-10*01": 1.0}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 8, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGGGGGGAATTCG", "dj_insertion": "T", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 351}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGGTACAAGTA-1_contig_2"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ5*02", "cdr3_length": 66, "mature_cdr3_lengths": [66], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATTGTTCAGGCGATTTTTGGAGTGGTTATTATCGATACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATTGTTCAGGCGATTTTTGGAGTGGTTATTATCGATACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9999999818677737, "IGHD3-9*01": 1.8132226392770897e-08}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 3, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTGTTCAGG", "dj_insertion": "CGAT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 351}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-69/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-69/igh.fa new file mode 100644 index 000000000..8168a295d --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-69/igh.fa @@ -0,0 +1,6 @@ +>AAACCTGAGTGAACAT-1_contig_2 +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAAACTCTCCTGTGCAGCCTCTGGATTCAGCCTCAACGACTACTATATGACCTGGATTCGCCAACCTCCAGGGAAGGGCCTGCAATGGCTTGCATACATCGATAATGTTGGAACAACCACATACTACGCAGACTCTCTGAGGGGCCGCTTCACCATCTCCAGGGACAACAGCAAAAACTCACTGTATCTGCAAATGGACGGCCTGACAGCCGAGGACACGGCCGTCTATTACTGTGCGCGAGATGGTTATTATGATTTTTGGAGTGGTAAATCAGATTATTATTATGGAATGGACCTCTGGGGCCAAGGGACCACGGTCATCGTCTCCTCAG +>AAACGGGAGCGTTGCC-1_contig_2 +CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCTACGTATTACTATGATAGTAGTGGTTATTACTCGGGTCTGGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>AAAGATGAGGACCACA-1_contig_2 +CAGGCGCAGCTGGAGGAGTCTGGGGGAGGCCTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGCTTCAGTTTCAGTACATATGTCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCGCTTGTCTCGTCTGACGGCAATGATAAATATTATGCAGACTCAGTGAAGGGCCGCTTCACTATCTCCAGAGACAATTCCAAGAACACTCTGGATCTGCAAATGAACAACATGAGAGGCGAGGACACGGCTGTCTATTACTGTGCGAGTGAACAACCCCTCTGGGGTGACTCCGTTGTCGGTTTCTTTTACTACGGAATGGACGTCTGGGGCCCAGGGACCACGGTCACCGTCTCTTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-69/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-69/partition-igh.yaml new file mode 100644 index 000000000..518db8f83 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-69/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -683.0811697848819, "n_clusters": 3, "n_procs": 1, "partition": [["AAACCTGAGTGAACAT-1_contig_2"], ["AAACGGGAGCGTTGCC-1_contig_2"], ["AAAGATGAGGACCACA-1_contig_2"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGAGTGAACAT-1_contig_2"], "invalid": false, "v_gene": "IGHV3-11*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ6*02", "cdr3_length": 69, "mature_cdr3_lengths": [69], "mut_freqs": [0.13246753246753246], "n_mutations": [51], "input_seqs": ["NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAAACTCTCCTGTGCAGCCTCTGGATTCAGCCTCAACGACTACTATATGACCTGGATTCGCCAACCTCCAGGGAAGGGCCTGCAATGGCTTGCATACATCGATAATGTTGGAACAACCACATACTACGCAGACTCTCTGAGGGGCCGCTTCACCATCTCCAGGGACAACAGCAAAAACTCACTGTATCTGCAAATGGACGGCCTGACAGCCGAGGACACGGCCGTCTATTACTGTGCGCGAGATGGTTATTATGATTTTTGGAGTGGTAAATCAGATTATTATTATGGAATGGACCTCTGGGGCCAAGGGACCACGGTCATCGTCTCCTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGATGGGTATTACGATTTTTGGAGTGGTTATTATACCTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-11*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.935947957342859, "IGHD3-10*01": 0.02445084739988633, "IGHD3-22*01": 0.02017908907269661, "IGHD3-9*01": 0.018548703117429254, "IGHD3-16*03": 0.0008734030671530159}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TGG", "dj_insertion": "", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 354}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACGGGAGCGTTGCC-1_contig_2"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ4*02", "cdr3_length": 69, "mature_cdr3_lengths": [69], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCTACGTATTACTATGATAGTAGTGGTTATTACTCGGGTCTGGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCTACGTATTACTATGATAGTAGTGGTTATTACTCGGGTCTGGGGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ4*02": 0.999999462052865, "IGHJ5*02": 5.379471380916758e-07}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 2, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CTAC", "dj_insertion": "CGGGTCTGGGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 354}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAAGATGAGGACCACA-1_contig_2"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD3-16*03", "j_gene": "IGHJ6*02", "cdr3_length": 69, "mature_cdr3_lengths": [69], "mut_freqs": [0.14025974025974025], "n_mutations": [54], "input_seqs": ["NNNCAGGCGCAGCTGGAGGAGTCTGGGGGAGGCCTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGCTTCAGTTTCAGTACATATGTCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCGCTTGTCTCGTCTGACGGCAATGATAAATATTATGCAGACTCAGTGAAGGGCCGCTTCACTATCTCCAGAGACAATTCCAAGAACACTCTGGATCTGCAAATGAACAACATGAGAGGCGAGGACACGGCTGTCTATTACTGTGCGAGTGAACAACCCCTCTGGGGTGACTCCGTTGTCGGTTTCTTTTACTACGGAATGGACGTCTGGGGCCCAGGGACCACGGTCACCGTCTCTTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGATTACATTTGGGGGAGTTATCGTTATACCTTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 0.9942215983242617, "IGHV3-30*04": 0.005778401675710008}, "d_per_gene_support": {"IGHD3-16*03": 0.7758896010469405, "IGHD2-21*01": 0.18781533949118226, "IGHD4-17*01": 0.03549526273066466, "IGHD6-19*01": 0.0006036155703397153, "IGHD7-27*01": 0.00019618116084292185}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 7, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "T", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 354}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-72/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-72/igh.fa new file mode 100644 index 000000000..69acf2cd5 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-72/igh.fa @@ -0,0 +1,2 @@ +>AAACCTGCAGGGTTAG-1_contig_2 +CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGAAGGAAGTACTATGATAGTAGTGGTGGCACCTATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-72/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-72/partition-igh.yaml new file mode 100644 index 000000000..be2c9e947 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-72/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -61.31433181422267, "n_clusters": 1, "n_procs": 1, "partition": [["AAACCTGCAGGGTTAG-1_contig_2"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGCAGGGTTAG-1_contig_2"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ6*02", "cdr3_length": 72, "mature_cdr3_lengths": [72], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGAAGGAAGTACTATGATAGTAGTGGTGGCACCTATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGAAGGAAGTACTATGATAGTAGTGGTGGCACCTATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 0.9999999837292323, "IGHD2-15*01": 8.43235270846447e-09, "IGHD6-19*01": 4.600117380528303e-09, "IGHD3-16*03": 2.536336762837154e-09, "IGHD3-3*01": 7.019590715268091e-10}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 2, "d_5p_del": 4, "d_3p_del": 9, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AGGAAG", "dj_insertion": "GGCACCT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 357}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-81/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-81/igh.fa new file mode 100644 index 000000000..234c27480 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-81/igh.fa @@ -0,0 +1,2 @@ +>AAACCTGTCCGGCACA-1_contig_3 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATGGGGTGATGTATGACTACGGTGACTACGTCCCTTTGCGGTTTTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-81/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-81/partition-igh.yaml new file mode 100644 index 000000000..a43349638 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-81/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -77.63248029375826, "n_clusters": 1, "n_procs": 1, "partition": [["AAACCTGTCCGGCACA-1_contig_3"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCCGGCACA-1_contig_3"], "invalid": false, "v_gene": "IGHV3-21*01", "d_gene": "IGHD4-17*01", "j_gene": "IGHJ6*02", "cdr3_length": 81, "mature_cdr3_lengths": [81], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATGGGGTGATGTATGACTACGGTGACTACGTCCCTTTGCGGTTTTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATGGGGTGATGTATGACTACGGTGACTACGTCCCTTTGCGGTTTTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-21*01": 1.0}, "d_per_gene_support": {"IGHD4-17*01": 0.9999994326981653, "IGHD3-22*01": 4.809730645322982e-07, "IGHD3-10*01": 8.544648466638764e-08, "IGHD2-21*01": 7.459581866952642e-10, "IGHD3-16*03": 1.3632142939706357e-10}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TGGGGTGATGTA", "dj_insertion": "GTCCCTTTGCGGTTT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 363}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-84/igh.fa b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-84/igh.fa new file mode 100644 index 000000000..28aaf8f50 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-84/igh.fa @@ -0,0 +1,2 @@ +>AAACCTGTCTGGCGAC-1_contig_1 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGGCCGACCCAGCAGCTGGTACTTGGGGCGAATAACCTGGCGGGGTGTCAACACTGACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-84/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-84/partition-igh.yaml new file mode 100644 index 000000000..d43a85ad3 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/groups/cdr3-84/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-46*03": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTTTCCTGCAAGGCATCTGGATACACCTTCACCAGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAATAATCAACCCTAGTGGTGGTAGCACAAGCTACGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGGACACGTCCACGAGCACAGTCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCTAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-8*01": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGG", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-15*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTTAGACTCTCCTGTGCAGCCTCTGGATTCACTTTCAGTAACGCCTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTGGCCGTATTAAAAGCAAAACTGATGGTGGGACAACAGACTACGCTGCACCCGTGAAAGGCAGATTCACCATCTCAAGAGATGATTCAAAAAACACGCTGTATCTGCAAATGAACAGCCTGAAAACCGAGGACACAGCCGTGTATTACTGTACCACAGA", "IGHV3-20*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGTGTGGTACGGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGGCATGAGCTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGAGTGGGTCTCTGGTATTAATTGGAATGGTGGTAGCACAGGTTATGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCCTTGTATCACTGTGCGAGAGA", "IGHV3-21*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCCTGGTCAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTAGTTACATATACTACGCAGACTCAGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-30*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATGCTATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATCATATGATGGAAGTAATAAATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-48*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTATAGCATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAATGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGACGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-66*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCAGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-74*01": "GAGGTGCAGCTGGTGGAGTCCGGGGGAGGCTTAGTTCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTAGCTACTGGATGCACTGGGTCCGCCAAGCTCCAGGGAAGGGGCTGGTGTGGGTCTCACGTATTAATAGTGATGGGAGTAGCACAAGCTACGCGGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACACGCTGTATCTGCAAATGAACAGTCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCAAGAGA", "IGHV3-9*01": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-31*03": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCACAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTGGTGGTTACTACTGGAGCTGGATCCGCCAGCACCCAGGGAAGGGCCTGGAGTGGATTGGGTACATCTATTACAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTTACCATATCAGTAGACACGTCTAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACTGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA", "IGHV4-4*02": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGGGACCCTGTCCCTCACCTGCGCTGTCTCTGGTGGCTCCATCAGCAGTAGTAACTGGTGGAGTTGGGTCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCTATCATAGTGGGAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACAAGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-59*11": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTCACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD1-7*01": "GGTATAACTGGAACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD5-24*01": "GTAGAGATGGCTACAATTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV3-74*01": 285, "IGHV2-5*02": 288, "IGHV4-59*11": 282, "IGHV3-9*01": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV3-21*01": 285, "IGHV2-70*01": 288, "IGHV1-18*01": 285, "IGHV4-31*03": 288, "IGHV3-7*01": 285, "IGHV3-11*01": 285, "IGHV3-30*04": 285, "IGHV3-66*01": 282, "IGHV1-8*01": 285, "IGHV4-39*01": 288, "IGHV1-46*03": 285, "IGHV3-23*01": 285, "IGHV3-15*01": 291, "IGHV3-20*01": 285, "IGHV3-48*02": 285, "IGHV4-4*02": 285}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18}}, "partitions": [{"logprob": -95.02909336062365, "n_clusters": 1, "n_procs": 1, "partition": [["AAACCTGTCTGGCGAC-1_contig_1"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["AAACCTGTCTGGCGAC-1_contig_1"], "invalid": false, "v_gene": "IGHV1-8*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ5*02", "cdr3_length": 84, "mature_cdr3_lengths": [84], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGGCCGACCCAGCAGCTGGTACTTGGGGCGAATAACCTGGCGGGGTGTCAACACTGACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCAGTTATGATATCAACTGGGTGCGACAGGCCACTGGACAAGGGCTTGAGTGGATGGGATGGATGAACCCTAACAGTGGTAACACAGGCTATGCACAGAAGTTCCAGGGCAGAGTCACCATGACCAGGAACACCTCCATAAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGGCCGACCCAGCAGCTGGTACTTGGGGCGAATAACCTGGCGGGGTGTCAACACTGACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-8*01": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9997784002751684, "IGHD6-19*01": 0.00021569296404276578, "IGHD6-6*01": 5.629811350480175e-06, "IGHD2-15*01": 2.76894401827468e-07, "IGHD1-1*01": 5.5024222184992535e-11}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGACC", "dj_insertion": "TTGGGGCGAATAACCTGGCGGGGTGTCAACACTG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 366}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-data/manifest.yaml b/test/paired/ref-results/disjoint-group-new-data/manifest.yaml new file mode 100644 index 000000000..631990573 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-data/manifest.yaml @@ -0,0 +1,158 @@ +assembly: + merged_output_path: assembled/ + status: merged + validation: + gene_lists_consistent: null + sequence_count_preserved: true + uids_unique: true +grouping-info: + failed_sequences: 0 + loci: + - igh + - igk + - igl + method: cdr3-length + parameter_dir: test/paired/ref-results/test/parameters/data + total_grouped_sequences: 100 + total_input_sequences: 100 +groups: +- cdr3_length: 30 + fasta_path: groups/cdr3-30/igh.fa + group_id: 0 + locus: igh + partition_path: groups/cdr3-30/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 36 + fasta_path: groups/cdr3-36/igh.fa + group_id: 1 + locus: igh + partition_path: groups/cdr3-36/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 39 + fasta_path: groups/cdr3-39/igh.fa + group_id: 2 + locus: igh + partition_path: groups/cdr3-39/partition-igh.yaml + sequence_count: 2 +- cdr3_length: 42 + fasta_path: groups/cdr3-42/igh.fa + group_id: 3 + locus: igh + partition_path: groups/cdr3-42/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 45 + fasta_path: groups/cdr3-45/igh.fa + group_id: 4 + locus: igh + partition_path: groups/cdr3-45/partition-igh.yaml + sequence_count: 6 +- cdr3_length: 48 + fasta_path: groups/cdr3-48/igh.fa + group_id: 5 + locus: igh + partition_path: groups/cdr3-48/partition-igh.yaml + sequence_count: 6 +- cdr3_length: 51 + fasta_path: groups/cdr3-51/igh.fa + group_id: 6 + locus: igh + partition_path: groups/cdr3-51/partition-igh.yaml + sequence_count: 8 +- cdr3_length: 54 + fasta_path: groups/cdr3-54/igh.fa + group_id: 7 + locus: igh + partition_path: groups/cdr3-54/partition-igh.yaml + sequence_count: 5 +- cdr3_length: 57 + fasta_path: groups/cdr3-57/igh.fa + group_id: 8 + locus: igh + partition_path: groups/cdr3-57/partition-igh.yaml + sequence_count: 2 +- cdr3_length: 60 + fasta_path: groups/cdr3-60/igh.fa + group_id: 9 + locus: igh + partition_path: groups/cdr3-60/partition-igh.yaml + sequence_count: 4 +- cdr3_length: 63 + fasta_path: groups/cdr3-63/igh.fa + group_id: 10 + locus: igh + partition_path: groups/cdr3-63/partition-igh.yaml + sequence_count: 2 +- cdr3_length: 66 + fasta_path: groups/cdr3-66/igh.fa + group_id: 11 + locus: igh + partition_path: groups/cdr3-66/partition-igh.yaml + sequence_count: 4 +- cdr3_length: 69 + fasta_path: groups/cdr3-69/igh.fa + group_id: 12 + locus: igh + partition_path: groups/cdr3-69/partition-igh.yaml + sequence_count: 3 +- cdr3_length: 72 + fasta_path: groups/cdr3-72/igh.fa + group_id: 13 + locus: igh + partition_path: groups/cdr3-72/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 81 + fasta_path: groups/cdr3-81/igh.fa + group_id: 14 + locus: igh + partition_path: groups/cdr3-81/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 84 + fasta_path: groups/cdr3-84/igh.fa + group_id: 15 + locus: igh + partition_path: groups/cdr3-84/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 30 + fasta_path: groups/cdr3-30/igk.fa + group_id: 0 + locus: igk + partition_path: groups/cdr3-30/partition-igk.yaml + sequence_count: 6 +- cdr3_length: 33 + fasta_path: groups/cdr3-33/igk.fa + group_id: 1 + locus: igk + partition_path: groups/cdr3-33/partition-igk.yaml + sequence_count: 21 +- cdr3_length: 36 + fasta_path: groups/cdr3-36/igk.fa + group_id: 2 + locus: igk + partition_path: groups/cdr3-36/partition-igk.yaml + sequence_count: 7 +- cdr3_length: 39 + fasta_path: groups/cdr3-39/igk.fa + group_id: 3 + locus: igk + partition_path: groups/cdr3-39/partition-igk.yaml + sequence_count: 3 +- cdr3_length: 33 + fasta_path: groups/cdr3-33/igl.fa + group_id: 0 + locus: igl + partition_path: groups/cdr3-33/partition-igl.yaml + sequence_count: 6 +- cdr3_length: 36 + fasta_path: groups/cdr3-36/igl.fa + group_id: 1 + locus: igl + partition_path: groups/cdr3-36/partition-igl.yaml + sequence_count: 3 +- cdr3_length: 39 + fasta_path: groups/cdr3-39/igl.fa + group_id: 2 + locus: igl + partition_path: groups/cdr3-39/partition-igl.yaml + sequence_count: 6 +version-info: + partis-yaml: 0.2 diff --git a/test/paired/ref-results/disjoint-group-new-simu/assembled/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-simu/assembled/partition-igh.yaml new file mode 100644 index 000000000..c08732d5e --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/assembled/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV2-70*01": 288, "IGHV3-7*01": 285, "IGHV4-39*01": 288}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17}}, "partitions": [{"logprob": 0.0, "n_clusters": 25, "n_procs": 1, "partition": [["db63559ea9-igh"], ["276733008f-igh"], ["3542bd38d8-igh"], ["35fc655801-igh", "7ba384a461-igh", "7d4166ae48-igh", "cfe3b29587-igh"], ["3c5f4c778a-igh"], ["52387a89c7-igh", "bb82ebe094-igh"], ["789d880ef2-igh"], ["a4b090d0be-igh", "e6fa048856-igh"], ["bc11af4843-igh"], ["09f5010bd3-igh", "eee6809ad6-igh"], ["14195e4958-igh", "8b9ef6b10e-igh", "e11acbe3ab-igh", "eee2c7797d-igh"], ["21cea6e4d0-igh", "57537e5f22-igh"], ["28ce45b82a-igh", "be186138e0-igh"], ["b739ce37b7-igh"], ["cb8a759f1a-igh"], ["3a07b6f0a9-igh", "7334912e1e-igh", "f094dfd68a-igh"], ["453132f3ab-igh"], ["b997fa9304-igh", "f3509e0ef3-igh"], ["0eb272ee70-igh", "9ed10b6475-igh", "aa25e6c0ce-igh"], ["253ca59333-igh", "ddcf0ca433-igh"], ["4d37fe487e-igh", "7588f09c07-igh"], ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh", "b02ee7754a-igh", "a2238f4e9a-igh"], ["28f6e090f2-igh", "584ba32878-igh", "b9148494e2-igh"], ["4f03967793-igh", "c2cc9da0c3-igh", "6cf028b770-igh", "6577576bb8-igh", "c0fcfe005f-igh", "d1ee7f9ce6-igh", "665985d2d1-igh"], ["7c67587674-igh", "cdae60eacc-igh"]]}], "events": [{"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["db63559ea9-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD2-8*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.07102272727272728], "n_mutations": [25], "input_seqs": ["CTGGTCACCTTGAGGGAGTTCGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTGCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGACAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGGACTCATTGATTGGGATGATCATAAATACTGCTGCGCAGCTCTGGCGACCAGGATCACCATCTCCAAGGACACCTCCAAGGACCAGCTGGTCCTTACAATGATCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTCATAATTGTGGACTTTTGGGGCCAGGGAACACTGGTTACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTACTAATGGTGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD2-8*01": 0.9545132386510512, "IGHD2-8*02": 0.01672841068859474, "IGHD2-15*01": 0.014568075322112222, "IGHD2-21*01": 0.007990205769238692, "IGHD2-2*01": 0.006200069568990947}, "j_per_gene_support": {"IGHJ4*02": 0.999992566973389, "IGHJ5*02": 7.433026603994982e-06}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 11, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 318}}, {"qr_gap_seqs": ["", "", "", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCAGTGTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["", "", "", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATC....TCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "", "", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["35fc655801-igh", "7ba384a461-igh", "7d4166ae48-igh", "cfe3b29587-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD7-27*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39, 39, 39], "mut_freqs": [0.00558659217877095, 0.00558659217877095, 0.0, 0.0], "n_mutations": [2, 2, 0, 0], "input_seqs": ["CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGCCGAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGCCGAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCAGTGTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, true], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], []], "leader_seqs": ["", "", "", ""], "c_gene_seqs": ["", "", "", ""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD7-27*01": 0.9986842497443288, "IGHD1-1*01": 0.0013083916860406383, "IGHD2-8*02": 4.305929134187837e-06, "IGHD3-16*03": 2.4922276307323943e-06, "IGHD2-2*01": 3.8802168232053814e-07, "IGHD3-9*01": 1.7239118405175848e-07}, "j_per_gene_support": {"IGHJ4*02": 0.9999990472820661, "IGHJ5*02": 9.527179352372375e-07}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCC", "dj_insertion": "CG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false], "in_frames": [true, true, true, true], "stops": [false, false, false, false], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["52387a89c7-igh", "bb82ebe094-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39], "mut_freqs": [0.07541899441340782, 0.0893854748603352], "n_mutations": [27, 32], "input_seqs": ["CCGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCTCTCAGCACTAGTGGCATGTGTGTGAGCTGGATCCGTCAGCCCGCAGGGCAGGCCCAGGAGGGGCTTGGACTCATTGATTGGGATGTTCATAAATACTACAGCACATCTCTGAGGAACAGGCTTACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATAACCAACATGGACCCTGTGGATACAGTAACGTATTACTGTGGACGGATACCCTCAATTTTGTACCTGGATTTCTGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCACCTTGAGGGAGTTTGGTCCTGCGCTGGTGAAATCCAGACAGATCCTCACCGTGACCTGGACCTTCTCTGGGTTCTCACTCGGCACTAATGGAATGTGTGTGAGCTGGAACCGTCAGCCCCCAGGAAAGGCCATGGAGTGGCTTGGACGCATTGATTGGGATGAGCATAAATACTACAGCACATCGCTGAAAAGCAGGCTCACCATCTCCAAGGACACCTCCAAACACCGGGTGGTCCTTACAATGACCAACATGAACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTATTGATTTTAGAACTTGATTACTGGGGCTAGGGAACCCTGTTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCTGGTTATTATACCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9987765312973691, "IGHD3-9*01": 0.0009020259961500695, "IGHD2-8*01": 0.00023352598138010188, "IGHD2-21*01": 4.480708795611879e-05, "IGHD2-15*01": 2.437252175713299e-05, "IGHD2-2*01": 1.8737115450187652e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999999740027764, "IGHJ5*02": 2.5997251241431484e-08}, "v_3p_del": 0, "d_5p_del": 18, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CC", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, true], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["a4b090d0be-igh", "e6fa048856-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-10*03", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39], "mut_freqs": [0.06983240223463687, 0.05307262569832402], "n_mutations": [25, 19], "input_seqs": ["CCGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCTCTCAGCACTAGTGGCATGTGTGTGAGCTGGATCCGTCAGCCCGCAGGGCAGGCCCAGGAGGGGCTTGGACTCATTGATTGGGATGATCATAAATACTACAGCACATCTCTGAAGAACAGACTTACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGATACAGTAACGTATTACTGTGGACGGATACCCTCAATCGTGTACTTGGATTTCTGGGCCCAGGGAACCCTGGTAACCGTCTCCTCAG", "CAGGTCATCTCGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGAACTGCACCTTCTCTGGGTTCTCACTCAGCACGAGTGGAATGTGTGTGAGCTTGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTTCACTCATAGATTGGGATGATCATAAATACTACAGCAAATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACGCCCAAAAACCAGGTGGTCCTTACAATGACCAACATGTACCCTGTGGACAAAGCCACGTCTTACTGTGCACGGATACCTACTATGGTGGAATTTGAACACTGGGGCCAGGGAACCCTGGTCAGCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCTACTATGGTGTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-10*03": 0.8607442180179671, "IGHD2-8*01": 0.11314377836256438, "IGHD1-26*01": 0.012391978706903718, "IGHD3-16*03": 0.005675776514860024, "IGHD2-2*01": 0.005231198365534917, "IGHD6-6*01": 0.0020015610173958285, "IGHD2-21*01": 0.0004353714887649871, "IGHD2-15*01": 0.00037611752603844027}, "j_per_gene_support": {"IGHJ4*02": 0.9999999120282478, "IGHJ5*02": 8.797175077085633e-08}, "v_3p_del": 0, "d_5p_del": 4, "d_3p_del": 18, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "C", "dj_insertion": "G", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["276733008f-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD2-8*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.05865921787709497], "n_mutations": [21], "input_seqs": ["CAGGTCACCTTGAGGGCGTCTGGTCCTGCGCTGCTGAAACCCACAAAGACCCTCACACTTACCTGCACCTTCTCTGGGTTCCCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGCGATGATCATAAATATTATACCACATCTCTTAAGACCCGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCCTACATTGACCAACATGGACCCTGTGAACACAGCCACGTATTACTGTGCACGGATACTCTCTACTATTGGTTTTGTTTACTGGGGCCAGGGTACCCTGGTCACCCTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTCTGTACTAATGGTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD2-8*01": 0.9461862037204629, "IGHD1-26*01": 0.030888698799681313, "IGHD2-8*02": 0.013695925534625229, "IGHD1-1*01": 0.0070928013998329455, "IGHD3-10*03": 0.0021363705454102645}, "j_per_gene_support": {"IGHJ4*02": 0.9999213816654228, "IGHJ5*02": 7.861833457443879e-05}, "v_3p_del": 0, "d_5p_del": 7, "d_3p_del": 12, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["3542bd38d8-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.08100558659217877], "n_mutations": [29], "input_seqs": ["CCGGTCACCTTGAGGGAGTCTGGTCCCGCGCTGGTTAAACCCACACAGACCCTCACACTGACCTGCAACTTCTCTGGGCTCTCACTCAGCACTAGTGTAATGCGTGTGAGCTGGATCCGTCAGCCCCCAAGGAAGGCCCTGGAGTGGGATGCACTCATTGTTTGGGATGATCATATATACTACAGCACATCTCTGAAGACCAGGCTCACTATCTCCAAGGACACCTCCACAAACCCGGTGGTCCTTACAATGACCAACATGGTCCCTGTGGATACAGCCACGTATTACTGTGCACTGATACTCGCGAATTTGGATTTAGATTACTGGGGCCACGGAACTCTGTTCACCGTCTCCTCAA"], "has_shm_indels": [false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTCGCGATTTTTGGAGTAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9902763725121576, "IGHD3-16*03": 0.008544451016388389, "IGHD1-1*01": 0.0007247982551016534, "IGHD3-9*01": 0.0003496191248750958, "IGHD2-15*01": 0.00010475909149021817}, "j_per_gene_support": {"IGHJ4*02": 0.9994642028610878, "IGHJ5*02": 0.0005357971389022287}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 12, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCG", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["3c5f4c778a-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD1-1*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.04748603351955307], "n_mutations": [17], "input_seqs": ["CAGGTCACCTTGAGGGCGTCTGGTCCTCCGCTGCTGAAACCCACAAAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCCCACTCAGCACGAGTGGAATGTGTGTGAGCTGGATCCTTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTCATTGGGATGCTCATAAATACTACAGCACATCTCTGAAGACCAAGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACCTGGACCCTGTGAACACAGCCACGTATTACTGTGCACGGATACTCCCAACTGTCGGTTTTGATTACTGGGGCCAGGGCACCCTGGTCACCCTCTCCTCAA"], "has_shm_indels": [false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTCCCAACTGTCGGTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD1-1*01": 0.517891281008128, "IGHD7-27*01": 0.46191566817742113, "IGHD2-2*01": 0.012422735949157162, "IGHD2-8*02": 0.007703350299090547, "IGHD3-9*01": 6.696456621221164e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999971915780251, "IGHJ5*02": 2.808421971259051e-06}, "v_3p_del": 0, "d_5p_del": 4, "d_3p_del": 7, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCC", "dj_insertion": "TCGGT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["789d880ef2-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-9*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.061452513966480445], "n_mutations": [22], "input_seqs": ["CAGGTCACCTTGAGGGAGTTTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCTCACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCTCTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGGACTCATTTATTGGTATGATCATAAATAATACGGCACATCGCTGAAGAGGAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGATCCTTACAATTACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTTCACGGATACACTAAAGTGTGACTGTTGATTCCTGGGGCCAGGGAACCCTGGTCACCGTATCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACACGATATTTTGACTGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-9*01": 0.8499003721779994, "IGHD1-26*01": 0.10106714858525212, "IGHD2-8*01": 0.02529728640881477, "IGHD6-19*01": 0.023363293418709654, "IGHD2-21*01": 0.00037189940922378195}, "j_per_gene_support": {"IGHJ4*02": 0.9994816824392659, "IGHJ5*02": 0.0005183175607342217}, "v_3p_del": 0, "d_5p_del": 5, "d_3p_del": 11, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["bc11af4843-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD2-2*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.055865921787709494], "n_mutations": [20], "input_seqs": ["CAGGTCAGCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTGTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCAAGGGAAGGCCCTGGAGTGGCTTGCCCTCATTGATTGGGATGATCATAAATACTACAGCAGGACTGTGAAGACCAGGCTCACCATCTTCCAGTACACCTCCAGAAAACAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTATGCAGAGTCAGCTTTGATTGCTGGGGCCAGGGAAGCCTGGTCACCGTGTCCCCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTATGCCGAGTCAGCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD2-2*01": 0.5930148960805628, "IGHD2-8*01": 0.22296426646393663, "IGHD2-8*02": 0.14448352952763707, "IGHD3-16*03": 0.023934849107146286, "IGHD3-10*03": 0.0156024588207227}, "j_per_gene_support": {"IGHJ4*02": 0.9999806387199804, "IGHJ5*02": 1.9361280021906524e-05}, "v_3p_del": 0, "d_5p_del": 25, "d_3p_del": 0, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GAGTCAG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"qr_gap_seqs": ["TTGGTGCAGCTGGTGGAGTCTGGGAGTGTATGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGGCTCTCATGGGCAGCCTCTGGATTCACCTTTACTAGCTATTTGATGAGCTGGGTTGGCCAGGCTCCAGGGAAGGGGCTGGAGTGCGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACTACTCTCCAGAGACAACGCCAAGAACTCACTGTATGTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGTCCATCCCCTGGTGGTCCTGTGTGGGGTGACTACTGGGGCCAGGGAATCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["GAGGTGCAGCTGGTGGAGTCTGG........GGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCA.TCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGCCTTCAGCTCGTGGTCCTGTGCGGGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["TTGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGGCTCTCATGGGCAGCCTCTGGATTCACCTTTACTAGCTATTTGATGAGCTGGGTTGGCCAGGCTCCAGGGAAGGGGCTGGAGTGCGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACTATCTCCAGAGACAACGCCAAGAACTCACTGTATGTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGTCCATCCCCTGGTGGTCCTGTGTGGGGTGACTACTGGGGCCAGGGAATCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["14195e4958-igh", "8b9ef6b10e-igh", "e11acbe3ab-igh", "eee2c7797d-igh"], "invalid": false, "v_gene": "IGHV3-7*01", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48, 48, 48, 48], "mut_freqs": [0.06318681318681318, 0.07417582417582418, 0.04395604395604396, 0.057692307692307696], "n_mutations": [23, 27, 16, 21], "input_seqs": ["TTGGTGCAGCTGGTGGAGTCTGGGAGTGTATGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGGCTCTCATGGGCAGCCTCTGGATTCACCTTTACTAGCTATTTGATGAGCTGGGTTGGCCAGGCTCCAGGGAAGGGGCTGGAGTGCGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACTACTCTCCAGAGACAACGCCAAGAACTCACTGTATGTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGTCCATCCCCTGGTGGTCCTGTGTGGGGTGACTACTGGGGCCAGGGAATCCTGGTCACCGTCTCCTCAG", "TAGCTGCAGCTGGCGGAGTCTGGGGGAGGCTTGGTCGAGTCTGGGGGGTCCATGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGTTTTTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATTAAGCAAGATGGAAGTGAGAAATTCTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTAACTGTATCTGCAAATGAACACCCTGAAAGCCGAGGACACGGCTGTGTATTATTGTGCGAGAGAGCGTTCAGCTCGGGGACATGAGCGGGCTGACTAGTGGGGCCAGGGAATCCTTGTCACCGTCTCCACAG", "TAGGTGCAGCCGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTACTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGTGGCTGGAGTGTGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCAGCTCCAGAGACAACACCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACCCGGCTGTGTATTACTGTGCGAGAGACCAATCTGCTAGTGGTCTTGGGCGGGGTGACTACTGGGGCCAGGGAAGCCTGGTCACCGTCTCCTCAG", "TAGGTGCAGCGGGTGGAGTATGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGAGCAGCCTCTGGATTCACCTTTACTAGCTATTGGATGAGCTGGGTCGGCCAGGCTCCAGGGAAGGGGCTGGAGTGTGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGCACTCTGTGAAGGGCCGACTCACCAGCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAATTGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGCAACCGGCTAGTGGTGTTTGGCGGGCTGAATACTGGGGCCAGGGAAGCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [true, false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGACCCTCCAGCTCGTGGTGCTGGGCGGGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], []], "leader_seqs": ["", "", "", ""], "c_gene_seqs": ["", "", "", ""], "v_per_gene_support": {"IGHV3-7*01": 1.0}, "d_per_gene_support": {"IGHD6-6*01": 0.8827811499304686, "IGHD2-8*02": 0.06315167177721374, "IGHD2-15*01": 0.030253089804588285, "IGHD2-2*01": 0.016670827265915837, "IGHD3-16*03": 0.002242430498400677, "IGHD2-21*01": 0.002201687961850952, "IGHD7-27*01": 0.001563147351145642, "IGHD1-14*01": 0.000716105570227255, "IGHD2-8*01": 0.000195851868502408, "IGHD3-10*03": 0.00019440052653640238, "IGHD1-26*01": 2.9637445145535326e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999934833721534, "IGHJ5*02": 6.516627850595669e-06}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 2, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCTC", "dj_insertion": "GGTGCTGGGCGGGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false], "in_frames": [true, true, true, true], "stops": [false, true, true, true], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": ["CAGGTCCAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGC............TGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTAGGGAGGTCAGGTAGGAGTGGATGGGAAGGATCATCCCTATCCGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTGGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGGTAAGCAGCCTTAGATCCGAGGACACGCTCGTGTATTACTGTGAGAGCCACCACGAGTTATGTCATAAAAATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTGCTCAG", ""], "gl_gap_seqs": ["CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTT...............GAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGCCGCCACGCGTTATACCATAAAACTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", ""], "indel_reversed_seqs": ["CAGGTCCAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGCCTGGGTCCTCGGTGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTGGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGGTAAGCAGCCTTAGATCCGAGGACACGCTCGTGTATTACTGTGAGAGCCACCACGAGTTATGTCATAAAAATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTGCTCAG", ""], "unique_ids": ["09f5010bd3-igh", "eee6809ad6-igh"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD3-16*03", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48, 48], "mut_freqs": [0.09065934065934066, 0.09065934065934066], "n_mutations": [33, 33], "input_seqs": ["CAGGTCCAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGCTGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTAGGGAGGTCAGGTAGGAGTGGATGGGAAGGATCATCCCTATCCGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTGGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGGTAAGCAGCCTTAGATCCGAGGACACGCTCGTGTATTACTGTGAGAGCCACCACGAGTTATGTCATAAAAATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTGCTCAG", "CAGGTCGAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGCCTGGGGCCTCGCTGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCTGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTTGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGCTAAGCAGCCTGAGATCCGAGGACACGGTCGTGTATAACTGTGAGAGCCGCAACACGTTATATCATAAAACTAACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTCCTCAG"], "has_shm_indels": [true, false], "naive_seq": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGCCGCCACGCGTTATACCATAAAACTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD3-16*03": 0.4900777076508471, "IGHD1-14*01": 0.4311215054514137, "IGHD3-3*01": 0.06508791962597235, "IGHD2-2*01": 0.006632268918067831, "IGHD3-10*03": 0.005661415592202817, "IGHD2-8*01": 0.0008411981499737442, "IGHD3-9*01": 0.0005779846114654471}, "j_per_gene_support": {"IGHJ4*02": 0.9999999999926672, "IGHJ5*02": 7.306826995028274e-12}, "v_3p_del": 3, "d_5p_del": 28, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGCCACG", "dj_insertion": "ATAAAACT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [true, true], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": ["TAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGTTCCCTGAGACTCTCCTGTGCAACCTCTGGATTCACCTTTAGTAGCTATT.GATGAGCAGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAATGGTTGGCCAACATAAAGTAAGATGGAAGTGAGAAATACTATCTGGACTCTGTGAAGGGCCGACTTACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGAATTCCGCTAGTGGACCTGTTATCGGTGACTCCTGGGGCCAGGGATTCCTGGTCTCCGTCTCCTCAG", ""], "gl_gap_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGGTCCCGCCAGTGCACCTGATACCGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", ""], "indel_reversed_seqs": ["TAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGTTCCCTGAGACTCTCCTGTGCAACCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCAGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAATGGTTGGCCAACATAAAGTAAGATGGAAGTGAGAAATACTATCTGGACTCTGTGAAGGGCCGACTTACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGAATTCCGCTAGTGGACCTGTTATCGGTGACTCCTGGGGCCAGGGATTCCTGGTCTCCGTCTCCTCAG", ""], "unique_ids": ["21cea6e4d0-igh", "57537e5f22-igh"], "invalid": false, "v_gene": "IGHV3-7*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48, 48], "mut_freqs": [0.06593406593406594, 0.06318681318681318], "n_mutations": [24, 23], "input_seqs": ["TAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGTTCCCTGAGACTCTCCTGTGCAACCTCTGGATTCACCTTTAGTAGCTATTGATGAGCAGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAATGGTTGGCCAACATAAAGTAAGATGGAAGTGAGAAATACTATCTGGACTCTGTGAAGGGCCGACTTACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGAATTCCGCTAGTGGACCTGTTATCGGTGACTCCTGGGGCCAGGGATTCCTGGTCTCCGTCTCCTCAG", "TAGGTGCAGCTTGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCATGTGCAGCCTCTCGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGGTCCAGGGAAGGGGCTGGAGTGGGTGGCCGAGATAAAGCAAGATGGTAGTCAGAAATACTATCTGGACTCACTGAAGGGCCGATTCACCAACTCCAGAGACAACGCCAAGACCTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGGGGTCCCGCCATTGCAACTGACACCGGTGACTACTGGGGCCAGGCAATCCTGGGCACCGTCTCCTCAG"], "has_shm_indels": [true, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGGTCCCGCCAGTGCACCTGATACCGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-7*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.5227152042607583, "IGHD3-16*03": 0.23763735026646135, "IGHD1-1*01": 0.21547281933764997, "IGHD1-14*01": 0.00955211669343816, "IGHD6-6*01": 0.008037545682559977, "IGHD7-27*01": 0.004264354294965131, "IGHD2-15*01": 0.0012297043482626727, "IGHD2-21*01": 0.0010880333202834625, "IGHD1-26*01": 2.100946699030204e-06, "IGHD3-9*01": 7.708488661446781e-07}, "j_per_gene_support": {"IGHJ4*02": 0.9999914368424356, "IGHJ5*02": 8.563157549740184e-06}, "v_3p_del": 0, "d_5p_del": 26, "d_3p_del": 0, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGGTCCCGCCAGTGCACCTG", "dj_insertion": "GG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [false, true], "stops": [true, true], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["28ce45b82a-igh", "be186138e0-igh"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48, 48], "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGCGTATAGTGGGAGCTACTACTTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGCGTATAGTGGGAGCTACTACTTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGCGTATAGTGGGAGCTACTACTTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD1-26*01": 0.9999999999994387, "IGHD2-15*01": 5.621796129949252e-13}, "j_per_gene_support": {"IGHJ4*02": 0.9999999998758256, "IGHJ5*02": 1.2417242399287063e-10}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GC", "dj_insertion": "TT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b739ce37b7-igh"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD2-21*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.07692307692307693], "n_mutations": [28], "input_seqs": ["CAGGTCCAGCTGATGCAGTCTTGGGCTGAGCTGAAGAAGCCTGTGTCCTCGCTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTAAGATATCAACTGTGTGCGACAGGCCCCTGGACAGGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACATCGCACAGAAGTTCCACGGCAGAGTCACGATTCCCGTGGAAATATACACGATGACAGCCTACATGGAGCTGAGCAGCATGAGATCCGGGGACACGGCCGTGTATTACTGTGGGAGATGACGGGAGGGAGATGGTGTTGATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTCTTCTCAC"], "has_shm_indels": [false], "naive_seq": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGATGACGGGAGGGAGATGGTGGTGATTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD2-21*01": 0.8236902394964637, "IGHD2-8*02": 0.09639164582468808, "IGHD1-26*01": 0.050222269119530816, "IGHD3-10*03": 0.018545432573660786, "IGHD2-8*01": 0.011150412985645676}, "j_per_gene_support": {"IGHJ4*02": 0.9999999532874437, "IGHJ5*02": 4.671254649868613e-08}, "v_3p_del": 2, "d_5p_del": 9, "d_3p_del": 9, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TGACGGGAGGGAGA", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": ["GAGGTGCAACTGGTGGCGTCTGGGGGAGGCTTGGACCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGCATTCACCTTTAGTTGCTATCGAATTCGCTGGGTCCGCCAGACTCAAGGGAAGGGGCT........TGGCTAACATAAAGCAAGATGCAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGTAAATGAACAGCCTGAGAGCCGAGGGCACGGCTGTGTCTTACTGTGCGCGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCTGCGAACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["GAGGTGCAACTGGTGGCGTCTGGGGGAGGCTTGGACCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGCATTCACCTTTAGTTGCTATCGAATTCGCTGGGTCCGCCAGACTCAAGGGAAGGGGCTGGAGTGGGTGGCTAACATAAAGCAAGATGCAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGTAAATGAACAGCCTGAGAGCCGAGGGCACGGCTGTGTCTTACTGTGCGCGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCTGCGAACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["cb8a759f1a-igh"], "invalid": false, "v_gene": "IGHV3-7*01", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.0521978021978022], "n_mutations": [19], "input_seqs": ["GAGGTGCAACTGGTGGCGTCTGGGGGAGGCTTGGACCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGCATTCACCTTTAGTTGCTATCGAATTCGCTGGGTCCGCCAGACTCAAGGGAAGGGGCTTGGCTAACATAAAGCAAGATGCAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGTAAATGAACAGCCTGAGAGCCGAGGGCACGGCTGTGTCTTACTGTGCGCGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCTGCGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [true], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-7*01": 1.0}, "d_per_gene_support": {"IGHD6-6*01": 0.8490602405645918, "IGHD3-16*03": 0.07978369326487597, "IGHD3-3*01": 0.03873207772642884, "IGHD1-1*01": 0.021785598637224474, "IGHD2-21*01": 0.010638389806893623}, "j_per_gene_support": {"IGHJ4*02": 0.9998907137850829, "IGHJ5*02": 0.00010928621492536946}, "v_3p_del": 1, "d_5p_del": 13, "d_3p_del": 0, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TACATTGCCCGAGTGCACG", "dj_insertion": "GCGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["3a07b6f0a9-igh", "7334912e1e-igh", "f094dfd68a-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD1-14*01", "j_gene": "IGHJ6*02", "cdr3_length": 54, "mature_cdr3_lengths": [54, 54, 54], "mut_freqs": [0.021621621621621623, 0.032432432432432434, 0.02702702702702703], "n_mutations": [8, 12, 10], "input_seqs": ["CAGGTGCAGCTGGTGGAATCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTGCTGTGCAGCGTCTGGATTCACCTTCAGTAGGTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGAGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGTTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGCCGGAACCGGAACAAATAGTTGCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTCTCCTTTTCAGCGTCTGGATTCACCTTCAGTAGGTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCATACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGTTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGTCCCGGCTGTGTATTACTGTGCGAGAGAGCCGGAACTGGTAGCACTAGTTCCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGGTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGGAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGTCACGGCTGTGGATTACTGTGCGAGAGGGCCGGCACCGGAACCGCTACTTACCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGGCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGGAACCGGAACCACTAGTTGCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD1-14*01": 0.9999938922735017, "IGHD1-1*01": 4.11644715461729e-06, "IGHD6-19*01": 1.8908934650875562e-06, "IGHD2-8*01": 8.500939069912918e-08, "IGHD2-15*01": 8.558489627512363e-09, "IGHD3-9*01": 6.274499552208029e-09, "IGHD1-26*01": 5.434974464376309e-10}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 5, "d_3p_del": 0, "j_5p_del": 13, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GCCGG", "dj_insertion": "TAGTTGC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 285, "j": 336}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["b997fa9304-igh", "f3509e0ef3-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD1-14*01", "j_gene": "IGHJ6*02", "cdr3_length": 54, "mature_cdr3_lengths": [54, 54], "mut_freqs": [0.013513513513513514, 0.021621621621621623], "n_mutations": [5, 8], "input_seqs": ["CTGGTTCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGAATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATCTGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGACACAGGAACCACGAGTTCGCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "CTAGTTCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGAATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATCTGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGACACAGGAACCACGAGTTTGCTACGATATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGACACAGGAACCACGAGTTCGCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD1-14*01": 0.9995170476475125, "IGHD1-1*01": 0.0003023948122658587, "IGHD3-3*01": 0.0001000888697622578, "IGHD3-16*03": 8.043259375141867e-05, "IGHD3-10*03": 3.6076719493621446e-08}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 13, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GCCGACACA", "dj_insertion": "GAGTTCG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 285, "j": 336}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["453132f3ab-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD1-14*01", "j_gene": "IGHJ6*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.016216216216216217], "n_mutations": [6], "input_seqs": ["CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACCCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGTCATGGACTGGGTCCGCCAGGCACCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAACAGGCAGCGGAACCAGAACTTTCCTACGGTATAGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAACAGGCACCGGAACCAGAACTTTCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD1-14*01": 0.9777748627165609, "IGHD1-1*01": 0.014925220630956105, "IGHD6-19*01": 0.0038088010013902092, "IGHD2-2*01": 0.0021935636128367383, "IGHD6-6*01": 0.0012975520382607676}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 1, "j_5p_del": 13, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "ACAGGC", "dj_insertion": "GAACTTTC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 336}}, {"qr_gap_seqs": ["", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGACCCCAGGTAAGGGGCTGGAGTGGATTGGGACTATCTATTACATTACTGGGAGCACCTACTACGACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCACCTACTTCCATCGCTCGAGACTTCTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "", "CAGCTGCAGCAGCAGGAGTCGGGCCCAAGGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGACTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGCTCGCGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTTCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAAGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGTGAGCACC.ACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACTCCCGCAGAAACGGCGGCGTATTACTGTGCGAGAAAGCAAAGCGACACAGTACCCCCCACTGTCCTCGAACGGGACTACTGGGGCCAGGGAACCCTGGTTACCGTCTCCTCAG"], "gl_gap_seqs": ["", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTA...TAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGGTCGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "CAGCTGCAGCTGCAGGAGTCGGGCCCA..GGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCAATGTATAGCAGTGGCTGGTACTGCCCTCGCTCGGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCAATGTATAGCAGTGGCTGGTACTGCCCTCGCTCGGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGACCCCAGGTAAGGGGCTGGAGTGGATTGGGACTATCTATTATACTGGGAGCACCTACTACGACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCACCTACTTCCATCGCTCGAGACTTCTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGACTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGCTCGCGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTTCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAAGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGTGAGCACCTACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACTCCCGCAGAAACGGCGGCGTATTACTGTGCGAGAAAGCAAAGCGACACAGTACCCCCCACTGTCCTCGAACGGGACTACTGGGGCCAGGGAACCCTGGTTACCGTCTCCTCAG"], "unique_ids": ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh", "b02ee7754a-igh", "a2238f4e9a-igh"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57, 57, 57, 57, 57], "mut_freqs": [0.06382978723404255, 0.08244680851063829, 0.07180851063829788, 0.07180851063829788, 0.09308510638297872], "n_mutations": [24, 31, 27, 27, 35], "input_seqs": ["CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGGTCGAGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGACCCCAGGTAAGGGGCTGGAGTGGATTGGGACTATCTATTACATTACTGGGAGCACCTACTACGACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCACCTACTTCCATCGCTCGAGACTTCTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTAAAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCTAGCAATGTAAAACAGTACCTCCTACGTCCATCGGTCGAGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCAGCAGGAGTCGGGCCCAAGGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGACTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGCTCGCGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTTCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAAGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGTGAGCACCACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACTCCCGCAGAAACGGCGGCGTATTACTGTGCGAGAAAGCAAAGCGACACAGTACCCCCCACTGTCCTCGAACGGGACTACTGGGGCCAGGGAACCCTGGTTACCGTCTCCTCAG"], "has_shm_indels": [false, true, false, true, true], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCAATGTATAGCAGTGGCTGGTACTGCCCTCGGTCGGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], []], "leader_seqs": ["", "", "", "", ""], "c_gene_seqs": ["", "", "", "", ""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9999999999988489, "IGHD6-6*01": 6.490582037650985e-13, "IGHD2-15*01": 4.798988703384929e-13, "IGHD1-14*01": 1.7611487621819817e-14, "IGHD2-2*01": 5.606341652198298e-15, "IGHD1-1*01": 2.8421573523526843e-15, "IGHD3-9*01": 1.1076997644552306e-17}, "j_per_gene_support": {"IGHJ4*02": 0.9999711015009162, "IGHJ5*02": 2.8898499086531146e-05}, "v_3p_del": 3, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CGAGCAAT", "dj_insertion": "TGCCCTCGGTCGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false], "in_frames": [true, true, true, true, true], "stops": [false, false, true, false, false], "codon_positions": {"v": 288, "j": 342}}, {"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["0eb272ee70-igh", "9ed10b6475-igh", "aa25e6c0ce-igh"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57, 57, 57], "mut_freqs": [0.07446808510638298, 0.06382978723404255, 0.05585106382978723], "n_mutations": [28, 24, 21], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGAAGTAGTAGTTCCTACTGGGGCCGGATCCGCCAGCCCCCAGGTAAGGGGGTGGAGTGGATTGGGAGTATCTATGATAGTGGTAGCACCTACTATAACCAGTCCCTCAAGAGTCGAGTCACCATATCTGTAGACGCGTCCAAGAAGCAGTTCTCCCTGAAGCTGAGCTCTGTGCCCGCCGCAGACACGGCTGCGTATTACTGTGCGAGAGAGTTGTGTATAGCAGTGCTTCTTGCTTGGATAGCCCCGGACTACTGGGGCTAGGGAACCCTGGTCACCGTCTCCTCTG", "CAGCTGCAGCTGCAGGAGTCGAGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTGTGGTGGCTCCATCAGCAGTAGTAGTTACGACTGGGGCTTGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGATTCACCATATCCGTAGAGCCGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCCGACACGGCTGCGTATTACTGTCCGAGTTAGCTTTGAATAGCAGTCCCTCGTACTTCGATATCACCGGACTACTGGGACAAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGAGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACGACTGGGGCTTGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGATTCACCATATCCGTAGACCCGTCCAAGAACCAGTTCTCCCTGAAGCTGCGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCAAACATTGAATAGCAGTATCTAGTACTTCGATAGCACCGGACTACTGGGACAAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCTTTGTATAGCAGTGGCTGGTACTTCGATAGCACCGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9999997620418809, "IGHD6-6*01": 2.3418504629794938e-07, "IGHD2-2*01": 1.988273350409855e-09, "IGHD2-8*02": 1.2264705818572036e-09, "IGHD1-14*01": 3.8112594239444925e-10, "IGHD2-21*01": 1.286873575664863e-10, "IGHD2-15*01": 3.520713912076132e-11, "IGHD2-8*01": 1.236345418720092e-11, "IGHD1-26*01": 8.472485990439427e-13, "IGHD3-9*01": 1.9268662352554875e-13}, "j_per_gene_support": {"IGHJ4*02": 0.9999999924384042, "IGHJ5*02": 7.561622846458987e-09}, "v_3p_del": 3, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CGAGCTTT", "dj_insertion": "TTCGATAGCACCG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [true, true, true], "codon_positions": {"v": 288, "j": 342}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["253ca59333-igh", "ddcf0ca433-igh"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57, 57], "mut_freqs": [0.05053191489361702, 0.047872340425531915], "n_mutations": [19, 18], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGTTGGCTCCATCAGCAGAAGTAGTTACTACTGCGGCCCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTCGGAGTATCTATTATAGTGGGAGCACCTACTACATCCAGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCCAACCATGCATATCAGTACCTCCTACTAAACTCTCGCAAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGTTGGCTCCATCAGCAGAAGTAGTTACTACTGCGGCCCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTCGGAGTATCTATTATAGTGGGAGCACCTACTACATCCAGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCCAGCCTTGCATATCAGTACCTCCTACAAAACTCTCGCAAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCCAGCCTTGCATAGCAGTGGCTGGTACTAAACTCTCGCAAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.8646456710709792, "IGHD2-21*01": 0.05203225393062207, "IGHD2-2*01": 0.046012716051568696, "IGHD6-6*01": 0.03384000877990313, "IGHD2-15*01": 0.0034682557233549536, "IGHD1-26*01": 1.0944435637735562e-06}, "j_per_gene_support": {"IGHJ4*02": 0.9999996327020249, "IGHJ5*02": 3.6729798603451555e-07}, "v_3p_del": 3, "d_5p_del": 4, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCAGCCTTGC", "dj_insertion": "TAAACTCTCGCAA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 288, "j": 342}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["4d37fe487e-igh", "7588f09c07-igh"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57, 57], "mut_freqs": [0.07712765957446809, 0.05319148936170213], "n_mutations": [29, 20], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGAACCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTATGGTGGCTCCATCACCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTCTTATAGTGGGAGCACATACTACAACCAGTCACTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCATGAACCAGTTCTCCCTGAAGCTGAGCTCTGTCACCGCCGCAGACACGGCTGCGTCTTACTGTGCGAGCCTGCCTAGAAGAGAAGTACCTCTTTATAAGATAGCTCAAGACTACTGGGACCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGAGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCAGTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGATGAGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCCCTCCTTGGATAGCAGGGCTTCGTTCAAAGATAGCACTAGACTACTGGGACCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCCCGCCTTGTATAGCAGTGGCTGGTACTAAGATAGCTCTAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9979158727162916, "IGHD3-16*03": 0.0011280460501943165, "IGHD6-6*01": 0.0008840090108589552, "IGHD2-2*01": 6.300312043410871e-05, "IGHD1-14*01": 8.049470041143693e-06, "IGHD2-8*01": 6.999707404741944e-07, "IGHD2-15*01": 3.191590394597858e-07, "IGHD3-10*03": 4.610745823863277e-10, "IGHD3-9*01": 4.131240482509177e-11}, "j_per_gene_support": {"IGHJ4*02": 0.99999985609379, "IGHJ5*02": 1.439061992227603e-07}, "v_3p_del": 3, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCGCCTT", "dj_insertion": "TAAGATAGCTCTA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 288, "j": 342}}, {"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["28f6e090f2-igh", "584ba32878-igh", "b9148494e2-igh"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ3*02", "cdr3_length": 63, "mature_cdr3_lengths": [63, 63, 63], "mut_freqs": [0.0, 0.0, 0.0], "n_mutations": [0, 0, 0], "input_seqs": ["CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "has_shm_indels": [false, false, false], "naive_seq": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD6-6*01": 0.9999992846753685, "IGHD6-19*01": 7.148231158165149e-07, "IGHD1-14*01": 4.882738422431044e-10, "IGHD2-15*01": 1.2872862335923694e-11, "IGHD1-26*01": 3.67709667430218e-13}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 2, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "ACCGGACTGCTCT", "dj_insertion": "CGATGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 285, "j": 345}}, {"qr_gap_seqs": ["", "", "", "CAGGTGTAGCTGATGGTGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTGACTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGCCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTATTATATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGAGGCGATTTGTGGAATGGTATTTTCGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["", "", "", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACT..CTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGCCGGGGGCGATTTTTGGAGTGGTTATTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["", "", "", "CAGGTGTAGCTGATGGTGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGCCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTATTATATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGAGGCGATTTGTGGAATGGTATTTTCGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["4f03967793-igh", "c2cc9da0c3-igh", "6cf028b770-igh", "6577576bb8-igh", "c0fcfe005f-igh", "d1ee7f9ce6-igh", "665985d2d1-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ5*02", "cdr3_length": 66, "mature_cdr3_lengths": [66, 66, 66, 66, 66, 66, 66], "mut_freqs": [0.060209424083769635, 0.06282722513089005, 0.06282722513089005, 0.049738219895287955, 0.034031413612565446, 0.028795811518324606, 0.034031413612565446], "n_mutations": [23, 24, 24, 19, 13, 11, 13], "input_seqs": ["CAGGTGCAGCTGATGGTGTCTGGGGGAGGCGGGGTCCAGCCGAGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCGGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAATTATATGGTATGATGGAAGTAACAAATACTATGCAGACTCCGTGAAGGGCTGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGGTGGAGGGGATCTCTGGACTGGTCTTTATGGGAACAACTGGTTCGACCCCTGGGGACAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGGGTCTGGGGGAGGCGTGGTCCAGCCTGGTAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTGACCTTATGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGAGTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAATTGAACAGCTTGAGAGCCGAGGAGACGGCTGTGAATTACTGTCCGAGAGAGGGTGGATTCGAATTATGGATTTGATAGTATGGTACCAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAT", "CAGGCGCAGCGGATGGAGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCAGGATTCACCTTCAGTAGCTATGGCATGCACCGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATCTTGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGACAAGCCTGAGAGCCGAGGACACGGATGTGAATTACTGTGCGAGAGATACTGGCGGCGATTTTTCGAATGGCCTTTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGTAGCTGATGGTGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTGACTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGCCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTATTATATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGAGGCGATTTGTGGAATGGTATTTTCGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGCGGAGTCTGGGGGAGGCGTGGTCCACCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCATCTGGATTCACCGTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTGCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCCGGGTGAGATTTTGGGTTTGGTTACTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCACCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCATCTGGATTCACCGTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGGTGAGATTTTGGGTTTGCTTACTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCACCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCATCTGGATTCACCGTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGGTTAGATTTTGGGTTTGGTTAGTGTGCGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, true, false, false, false], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGCTGGGGGCGATTTTTGGAGTGGTTATTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9999999999983515, "IGHD7-27*01": 8.308376385077691e-13, "IGHD3-16*03": 6.948266534158579e-13, "IGHD6-19*01": 1.3360536198414565e-13, "IGHD2-8*02": 6.433253481148827e-15, "IGHD2-15*01": 4.265508477870675e-15, "IGHD2-2*01": 2.4756584348163524e-15, "IGHD2-8*01": 2.2742933639680054e-15, "IGHD3-9*01": 1.8099647951750524e-15, "IGHD2-21*01": 1.7532292880581524e-15, "IGHD3-10*03": 4.237639904204738e-16}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 3, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGCTGGGGG", "dj_insertion": "GGGA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [true, true, false, true, true, true, true], "codon_positions": {"v": 285, "j": 348}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["7c67587674-igh", "cdae60eacc-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ5*02", "cdr3_length": 66, "mature_cdr3_lengths": [66, 66], "mut_freqs": [0.028795811518324606, 0.028795811518324606], "n_mutations": [11, 11], "input_seqs": ["CGGGTGCAGCTGATGGAGTCTGGGGGAGGCGTGGTACAGCCTGGGAGGTCCCTGAGACTCTCCTATGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCGGCCAGGCTCCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATGCGCCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGATGCGTTTTTTGGAATGGTCCGTCAAGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CGGGTGCAGCTGATGGAGTCTGGGGGAGGCGTGGTACAGCCTGGGAGGTCCCTGAGACTCTCCTATGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCGGCCAGGCTCCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATGCGCCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGATGCGTTTTTTGGAATGGTCCGTCAAGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGCTGGATGCGTTTTTTGGAGTGGTCCGTCAAGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9997233702522996, "IGHD6-19*01": 0.00023668470338459078, "IGHD2-8*01": 2.8778508903320612e-05, "IGHD3-9*01": 7.920884587635916e-06, "IGHD2-15*01": 3.2456508168783846e-06}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 9, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGCTGGATGCGT", "dj_insertion": "CCGTCAAGGA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 285, "j": 348}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/assembled/partition-igk.yaml b/test/paired/ref-results/disjoint-group-new-simu/assembled/partition-igk.yaml new file mode 100644 index 000000000..a10b9e430 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/assembled/partition-igk.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-33*01": 261, "IGKV3-11*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV2-30*01": 276}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 6, "n_procs": 1, "partition": [["35fc655801-igk", "51c4c0cd70-igk", "7ba384a461-igk"], ["276733008f-igk", "3542bd38d8-igk", "3c5f4c778a-igk", "52387a89c7-igk", "789d880ef2-igk", "83d3e14e07-igk", "a4b090d0be-igk", "bc11af4843-igk", "cfe3b29587-igk", "db63559ea9-igk", "e2bf2000dd-igk", "e6fa048856-igk", "bb82ebe094-igk"], ["28ce45b82a-igk", "be186138e0-igk"], ["28f6e090f2-igk", "b9148494e2-igk"], ["3a07b6f0a9-igk", "4219142930-igk", "453132f3ab-igk", "7334912e1e-igk", "9c1dc5e656-igk", "f094dfd68a-igk", "f3509e0ef3-igk"], ["4f03967793-igk", "6577576bb8-igk", "665985d2d1-igk", "6cf028b770-igk", "7c67587674-igk", "c0fcfe005f-igk", "c2cc9da0c3-igk", "cdae60eacc-igk", "d1ee7f9ce6-igk"]]}], "events": [{"qr_gap_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCAGCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "", ""], "gl_gap_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCC..CAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "", ""], "indel_reversed_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "", ""], "unique_ids": ["35fc655801-igk", "51c4c0cd70-igk", "7ba384a461-igk"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 30, "mature_cdr3_lengths": [30, 30, 30], "mut_freqs": [0.0, 0.0, 0.0], "n_mutations": [0, 0, 0], "input_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCAGCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "has_shm_indels": [true, false, false], "naive_seq": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGKV3-15*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ1*01": 1.0}, "v_3p_del": 6, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [false, true, true], "stops": [false, false, false], "codon_positions": {"v": 261, "j": 288}}, {"qr_gap_seqs": ["GATGTTGTGATGACTCAGTCTCCACT....CTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAACCTCGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTTGTGGTAATAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTAATACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACAAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTCGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCA.......GTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCAAATTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTAGACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "", "", "", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGC..................GGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGG....GGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "GATGTTGTGATGAAGTTTTAGTCTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATCCAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAAACTCCAAGGC....................................ACCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATAAAAC"], "gl_gap_seqs": ["GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTC.........TAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGG..ACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "", "", "", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "GATGTTGTGATGA.........CTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC"], "indel_reversed_seqs": ["GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAACCTCGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTAATACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACAAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTCGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCAAATTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTAGACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "", "", "", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "GATGTTGTGATGACTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATCCAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAAACTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGACCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATAAAAC"], "unique_ids": ["276733008f-igk", "3542bd38d8-igk", "3c5f4c778a-igk", "52387a89c7-igk", "789d880ef2-igk", "83d3e14e07-igk", "a4b090d0be-igk", "bc11af4843-igk", "cfe3b29587-igk", "db63559ea9-igk", "e2bf2000dd-igk", "e6fa048856-igk", "bb82ebe094-igk"], "invalid": false, "v_gene": "IGKV2-30*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ2*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33], "mut_freqs": [0.026706231454005934, 0.017804154302670624, 0.017804154302670624, 0.011869436201780416, 0.02373887240356083, 0.01483679525222552, 0.017804154302670624, 0.026706231454005934, 0.002967359050445104, 0.011869436201780416, 0.01483679525222552, 0.01483679525222552, 0.020771513353115726], "n_mutations": [9, 6, 6, 4, 8, 5, 6, 9, 1, 4, 5, 5, 7], "input_seqs": ["GATGTTGTGATGACTCAGTCTCCACTCTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAACCTCGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTTGTGGTAATAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTAATACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACAAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTCGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCAAATTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTAGACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATTTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTATTACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCAGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATTGAAACACCTAATTGAATTGGTTTCAGCAGAGGCGAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGCTGTGATGACTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCTTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGTAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTAGAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACACATTCAGCGGCAGTGGGTAAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTTAGTCTCCACTCTCCCTGCTCGTCACCCTTGGACAGCCGGCCTCCATCTGCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTAGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCACCCTGCCCGTCACCCTTGGACAGCAGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATTGAAACACCTAATTGAATTGGTTTCAGCAGAGGCGAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACTGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACGGTGATCGAAACACCTACTTGAATTGGTTCCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTCGACACTGAAAATCAGAAGGGTGGAGGCTGAGGATGGTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGACCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATTTTGTGATGACTCAGTCTCCACTCTCCCTGCCGGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATACGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAACCCTCGTATACAGTGATTGAAACACCTACTTGAATTGGTTTCAGCAGAGGCGAGGCCAAACTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGCGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCATGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCACGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGCGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGACAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGAAGTTTTAGTCTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATCCAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAAACTCCAAGGCACCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATAAAAC"], "has_shm_indels": [true, true, false, false, false, false, false, false, true, false, false, false, true], "naive_seq": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "duplicates": [[], [], [], [], [], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGKV2-30*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ2*01": 1.0, "IGKJ1*01": 2.5632061055214944e-20}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, true, true, true, true], "stops": [true, true, false, true, true, true, true, false, false, false, true, false, true], "codon_positions": {"v": 276, "j": 306}}, {"qr_gap_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCGCACATGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGGGACTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCT...TCAGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAACGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCGCTTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGG...CGACTGGAGATTAAAC", "", ""], "gl_gap_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTC.....TGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAG....TGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAA.GCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATC...TGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", ""], "indel_reversed_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCAGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", ""], "unique_ids": ["3a07b6f0a9-igk", "4219142930-igk", "453132f3ab-igk", "7334912e1e-igk", "9c1dc5e656-igk", "f094dfd68a-igk", "f3509e0ef3-igk"], "invalid": false, "v_gene": "IGKV1-33*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ5*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33, 33, 33, 33, 33], "mut_freqs": [0.0, 0.0, 0.003105590062111801, 0.0, 0.0, 0.003105590062111801, 0.0], "n_mutations": [0, 0, 1, 0, 0, 1, 0], "input_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCGCACATGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGGGACTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTTCAGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAACGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCGCTTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGCGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGCCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"], "has_shm_indels": [true, false, true, false, true, false, false], "naive_seq": "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGKV1-33*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ5*01": 1.0}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GC", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [false, false, false, false, false, false, false], "codon_positions": {"v": 276, "j": 306}}, {"qr_gap_seqs": ["", "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCC...GGACCAAAGTGGATATCAAAC"], "gl_gap_seqs": ["", "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC"], "indel_reversed_seqs": ["", "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC"], "unique_ids": ["28ce45b82a-igk", "be186138e0-igk"], "invalid": false, "v_gene": "IGKV1D-13*02", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ3*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33], "mut_freqs": [0.0, 0.003105590062111801], "n_mutations": [0, 1], "input_seqs": ["NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCGGACCAAAGTGGATATCAAAC"], "has_shm_indels": [false, true], "naive_seq": "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGKV1D-13*02": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ3*01": 1.0}, "v_3p_del": 4, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GG", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 276, "j": 306}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["28f6e090f2-igk", "b9148494e2-igk"], "invalid": false, "v_gene": "IGKV3-11*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33], "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["NNNNNNNNNNNNNNNGAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "NNNNNNNNNNNNNNNGAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "has_shm_indels": [false, false], "naive_seq": "NNNNNNNNNNNNNNNGAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGKV3-11*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ1*01": 0.9999999999738236, "IGKJ4*01": 2.6173779204110916e-11}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 276, "j": 306}}, {"qr_gap_seqs": ["GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAA....................GCGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCATAAGGCGACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "", "", "", "", ""], "gl_gap_seqs": ["GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCA.......ACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "", "", "", "", ""], "indel_reversed_seqs": ["GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTGCGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "", "", "", "", ""], "unique_ids": ["4f03967793-igk", "6577576bb8-igk", "665985d2d1-igk", "6cf028b770-igk", "7c67587674-igk", "c0fcfe005f-igk", "c2cc9da0c3-igk", "cdae60eacc-igk", "d1ee7f9ce6-igk"], "invalid": false, "v_gene": "IGKV1-33*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 36, "mature_cdr3_lengths": [36, 36, 36, 36, 36, 36, 36, 36, 36], "mut_freqs": [0.003076923076923077, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "n_mutations": [1, 0, 0, 0, 0, 0, 0, 0, 0], "input_seqs": ["GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAGCGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCATAAGGCGACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "has_shm_indels": [true, false, true, false, false, false, false, false, false], "naive_seq": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGKV1-33*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 1.0}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "G", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true], "stops": [false, false, false, false, false, false, false, false, false], "codon_positions": {"v": 261, "j": 294}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/assembled/partition-igl.yaml b/test/paired/ref-results/disjoint-group-new-simu/assembled/partition-igl.yaml new file mode 100644 index 000000000..b0a4a9325 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/assembled/partition-igl.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"}}, "cyst-positions": {"IGLV2-14*04": 267, "IGLV2-23*02": 267, "IGLV1-40*01": 267}, "phen-positions": {"IGLJ1*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": 0.0, "n_clusters": 3, "n_procs": 1, "partition": [["09f5010bd3-igl", "b739ce37b7-igl", "eee6809ad6-igl"], ["0eb272ee70-igl", "253ca59333-igl", "4d37fe487e-igl", "7588f09c07-igl", "8d79fca804-igl", "a2238f4e9a-igl", "a3baa83300-igl", "aa25e6c0ce-igl", "b02ee7754a-igl", "b1e56e40a1-igl", "d5ddf0c2ec-igl", "ddcf0ca433-igl"], ["14195e4958-igl", "20909c3943-igl", "21cea6e4d0-igl", "57537e5f22-igl", "8807c8ff04-igl", "971ac047ee-igl"]]}], "events": [{"qr_gap_seqs": ["", "", "CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "gl_gap_seqs": ["", "", "CAGTCTGCCCTG...ACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["", "", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["09f5010bd3-igl", "b739ce37b7-igl", "eee6809ad6-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33], "mut_freqs": [0.0, 0.0, 0.0], "n_mutations": [0, 0, 0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false, false, true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGLV2-23*02": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ1*01": 1.0}, "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 267, "j": 297}}, {"qr_gap_seqs": ["", "", "", "", "", "", "", "", "", "", "", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGAT........TCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "gl_gap_seqs": ["", "", "", "", "", "", "", "", "", "", "", "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", "", "", "", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["0eb272ee70-igl", "253ca59333-igl", "4d37fe487e-igl", "7588f09c07-igl", "8d79fca804-igl", "a2238f4e9a-igl", "a3baa83300-igl", "aa25e6c0ce-igl", "b02ee7754a-igl", "b1e56e40a1-igl", "d5ddf0c2ec-igl", "ddcf0ca433-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39], "mut_freqs": [0.029940119760479042, 0.014970059880239521, 0.03293413173652695, 0.023952095808383235, 0.029940119760479042, 0.020958083832335328, 0.02694610778443114, 0.029940119760479042, 0.023952095808383235, 0.023952095808383235, 0.023952095808383235, 0.020958083832335328], "n_mutations": [10, 5, 11, 8, 10, 7, 9, 10, 8, 8, 8, 7], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACAGCGGGGCAGGTTATGATGTAAACTGGTACCAGCTGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGTCCATCACAGGGCTCCAGGTAGAGGATGAGGCTGATTATTACTGCAAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCAGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTAGGAGCAGCTCCAACATCGGTGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCATGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGCTGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCACAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTAATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCGTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCGAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCGCCAAGTCTGGCACCTCGGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCGTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTCGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGAACCTCCGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTGCTGCCAGTCCTTTGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCGGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "has_shm_indels": [false, false, false, false, false, false, false, false, false, false, false, true], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGLV1-40*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ1*01": 1.0}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, true, true, true], "stops": [true, true, true, true, true, true, true, true, true, true, true, true], "codon_positions": {"v": 267, "j": 303}}, {"qr_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", "", "", "", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCA........GCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", "", "", "", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATC.GCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", "", "", "", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "unique_ids": ["14195e4958-igl", "20909c3943-igl", "21cea6e4d0-igl", "57537e5f22-igl", "8807c8ff04-igl", "971ac047ee-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39, 39, 39, 39, 39], "mut_freqs": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "n_mutations": [0, 0, 0, 0, 0, 0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "has_shm_indels": [true, false, false, false, false, true], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", ""], "v_per_gene_support": {"IGLV2-14*04": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 1.0}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true], "stops": [false, false, false, false, false, false], "codon_positions": {"v": 267, "j": 303}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-30/igk.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-30/igk.fa new file mode 100644 index 000000000..7c599bcca --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-30/igk.fa @@ -0,0 +1,6 @@ +>7ba384a461-igk +GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>51c4c0cd70-igk +GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>35fc655801-igk +GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCAGCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-30/partition-igk.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-30/partition-igk.yaml new file mode 100644 index 000000000..0af1a4974 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-30/partition-igk.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-33*01": 261, "IGKV3-11*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV2-30*01": 276}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": -156.29533178930703, "n_clusters": 1, "n_procs": 1, "partition": [["35fc655801-igk", "51c4c0cd70-igk", "7ba384a461-igk"]]}], "events": [{"has_shm_indels": [true, false, false], "qr_gap_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCAGCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "", ""], "gl_gap_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCC..CAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "", ""], "indel_reversed_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "", ""], "unique_ids": ["35fc655801-igk", "51c4c0cd70-igk", "7ba384a461-igk"], "invalid": false, "v_gene": "IGKV3-15*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 30, "mature_cdr3_lengths": [30, 30, 30], "mut_freqs": [0.0, 0.0, 0.0], "n_mutations": [0, 0, 0], "input_seqs": ["GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCAGCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "naive_seq": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGKV3-15*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ1*01": 1.0}, "v_3p_del": 6, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [false, true, true], "stops": [false, false, false], "codon_positions": {"v": 261, "j": 288}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/igh.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/igh.fa new file mode 100644 index 000000000..4c09dc054 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/igh.fa @@ -0,0 +1,2 @@ +>db63559ea9-igh +CTGGTCACCTTGAGGGAGTTCGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTGCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGACAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGGACTCATTGATTGGGATGATCATAAATACTGCTGCGCAGCTCTGGCGACCAGGATCACCATCTCCAAGGACACCTCCAAGGACCAGCTGGTCCTTACAATGATCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTCATAATTGTGGACTTTTGGGGCCAGGGAACACTGGTTACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/igk.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/igk.fa new file mode 100644 index 000000000..1adb33e25 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/igk.fa @@ -0,0 +1,48 @@ +>3542bd38d8-igk +GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTCGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCAAATTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTAGACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>83d3e14e07-igk +GATGTTGTGATGACTTAGTCTCCACTCTCCCTGCTCGTCACCCTTGGACAGCCGGCCTCCATCTGCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTAGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>bc11af4843-igk +GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACGGTGATCGAAACACCTACTTGAATTGGTTCCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTCGACACTGAAAATCAGAAGGGTGGAGGCTGAGGATGGTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGACCAAAC +>e6fa048856-igk +GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCATGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCACGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGCGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGACAGGGGACCAAGCTGGAGATCAAAC +>e2bf2000dd-igk +GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAACCCTCGTATACAGTGATTGAAACACCTACTTGAATTGGTTTCAGCAGAGGCGAGGCCAAACTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGCGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>789d880ef2-igk +GATGCTGTGATGACTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCTTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGTAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTAGAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACACATTCAGCGGCAGTGGGTAAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>52387a89c7-igk +GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCAGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATTGAAACACCTAATTGAATTGGTTTCAGCAGAGGCGAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>a4b090d0be-igk +GATGTTGTGATGACTCAGTCTCCACTCACCCTGCCCGTCACCCTTGGACAGCAGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATTGAAACACCTAATTGAATTGGTTTCAGCAGAGGCGAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACTGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>db63559ea9-igk +GATTTTGTGATGACTCAGTCTCCACTCTCCCTGCCGGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATACGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>3c5f4c778a-igk +GATTTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTATTACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>276733008f-igk +GATGTTGTGATGACTCAGTCTCCACTCTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAACCTCGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTTGTGGTAATAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTAATACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACAAAGCTGGAGATCAAAC +>bb82ebe094-igk +GATGTTGTGATGAAGTTTTAGTCTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATCCAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAAACTCCAAGGCACCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATAAAAC +>b9148494e2-igk +GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>28f6e090f2-igk +GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC +>be186138e0-igk +GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCGGACCAAAGTGGATATCAAAC +>28ce45b82a-igk +GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC +>cfe3b29587-igk +GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC +>4219142930-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC +>f3509e0ef3-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC +>453132f3ab-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTTCAGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAACGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC +>9c1dc5e656-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCGCTTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGCGACTGGAGATTAAAC +>f094dfd68a-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGCCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC +>3a07b6f0a9-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCGCACATGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGGGACTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC +>7334912e1e-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/igl.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/igl.fa new file mode 100644 index 000000000..c4eea4cf7 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/igl.fa @@ -0,0 +1,6 @@ +>b739ce37b7-igl +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>eee6809ad6-igl +CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>09f5010bd3-igl +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igh.yaml new file mode 100644 index 000000000..913c9bc48 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV2-70*01": 288, "IGHV3-7*01": 285, "IGHV4-39*01": 288}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17}}, "partitions": [{"logprob": -130.3461290785209, "n_clusters": 1, "n_procs": 1, "partition": [["db63559ea9-igh"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["db63559ea9-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD2-8*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.07102272727272728], "n_mutations": [25], "input_seqs": ["CTGGTCACCTTGAGGGAGTTCGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTGCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGACAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGGACTCATTGATTGGGATGATCATAAATACTGCTGCGCAGCTCTGGCGACCAGGATCACCATCTCCAAGGACACCTCCAAGGACCAGCTGGTCCTTACAATGATCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTCATAATTGTGGACTTTTGGGGCCAGGGAACACTGGTTACCGTCTCCTCAG"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTACTAATGGTGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD2-8*01": 0.9545132386510512, "IGHD2-8*02": 0.01672841068859474, "IGHD2-15*01": 0.014568075322112222, "IGHD2-21*01": 0.007990205769238692, "IGHD2-2*01": 0.006200069568990947}, "j_per_gene_support": {"IGHJ4*02": 0.999992566973389, "IGHJ5*02": 7.433026603994982e-06}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 11, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 318}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igk.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igk.yaml new file mode 100644 index 000000000..5d8e0aa01 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igk.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-33*01": 261, "IGKV3-11*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV2-30*01": 276}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": -1614.2541300002924, "n_clusters": 5, "n_procs": 1, "partition": [["276733008f-igk", "3542bd38d8-igk", "3c5f4c778a-igk", "52387a89c7-igk", "789d880ef2-igk", "83d3e14e07-igk", "a4b090d0be-igk", "bc11af4843-igk", "cfe3b29587-igk", "db63559ea9-igk", "e2bf2000dd-igk", "e6fa048856-igk"], ["28ce45b82a-igk", "be186138e0-igk"], ["28f6e090f2-igk", "b9148494e2-igk"], ["3a07b6f0a9-igk", "4219142930-igk", "453132f3ab-igk", "7334912e1e-igk", "9c1dc5e656-igk", "f094dfd68a-igk", "f3509e0ef3-igk"], ["bb82ebe094-igk"]]}, {"logprob": -1609.08729721804, "n_clusters": 4, "n_procs": 1, "partition": [["276733008f-igk", "3542bd38d8-igk", "3c5f4c778a-igk", "52387a89c7-igk", "789d880ef2-igk", "83d3e14e07-igk", "a4b090d0be-igk", "bc11af4843-igk", "cfe3b29587-igk", "db63559ea9-igk", "e2bf2000dd-igk", "e6fa048856-igk", "bb82ebe094-igk"], ["28ce45b82a-igk", "be186138e0-igk"], ["28f6e090f2-igk", "b9148494e2-igk"], ["3a07b6f0a9-igk", "4219142930-igk", "453132f3ab-igk", "7334912e1e-igk", "9c1dc5e656-igk", "f094dfd68a-igk", "f3509e0ef3-igk"]]}], "events": [{"has_shm_indels": [true, true, false, false, false, false, false, false, true, false, false, false, true], "qr_gap_seqs": ["GATGTTGTGATGACTCAGTCTCCACT....CTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAACCTCGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTTGTGGTAATAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTAATACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACAAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTCGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCA.......GTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCAAATTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTAGACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "", "", "", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGC..................GGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGG....GGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "GATGTTGTGATGAAGTTTTAGTCTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATCCAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAAACTCCAAGGC....................................ACCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATAAAAC"], "gl_gap_seqs": ["GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTC.........TAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGG..ACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "", "", "", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "GATGTTGTGATGA.........CTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC"], "indel_reversed_seqs": ["GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAACCTCGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTAATACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACAAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTCGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCAAATTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTAGACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "", "", "", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "", "", "", "GATGTTGTGATGACTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATCCAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAAACTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGACCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATAAAAC"], "unique_ids": ["276733008f-igk", "3542bd38d8-igk", "3c5f4c778a-igk", "52387a89c7-igk", "789d880ef2-igk", "83d3e14e07-igk", "a4b090d0be-igk", "bc11af4843-igk", "cfe3b29587-igk", "db63559ea9-igk", "e2bf2000dd-igk", "e6fa048856-igk", "bb82ebe094-igk"], "invalid": false, "v_gene": "IGKV2-30*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ2*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33], "mut_freqs": [0.026706231454005934, 0.017804154302670624, 0.017804154302670624, 0.011869436201780416, 0.02373887240356083, 0.01483679525222552, 0.017804154302670624, 0.026706231454005934, 0.002967359050445104, 0.011869436201780416, 0.01483679525222552, 0.01483679525222552, 0.020771513353115726], "n_mutations": [9, 6, 6, 4, 8, 5, 6, 9, 1, 4, 5, 5, 7], "input_seqs": ["GATGTTGTGATGACTCAGTCTCCACTCTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAACCTCGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTTGTGGTAATAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTAATACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACAAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTCGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAGTATACAGTGAAGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCAAATTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTAGACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATTTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCCCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATTAGCAGGGTGGAGGCTGAAGATGTTGGGGTTTATTACTGCATGCAAGGTACACTCTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCAGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATTGAAACACCTAATTGAATTGGTTTCAGCAGAGGCGAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGCTGTGATGACTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCTTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGTAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTAGAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACACATTCAGCGGCAGTGGGTAAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTTAGTCTCCACTCTCCCTGCTCGTCACCCTTGGACAGCCGGCCTCCATCTGCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTAGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCACCCTGCCCGTCACCCTTGGACAGCAGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATTGAAACACCTAATTGAATTGGTTTCAGCAGAGGCGAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACTGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACGGTGATCGAAACACCTACTTGAATTGGTTCCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTCGACACTGAAAATCAGAAGGGTGGAGGCTGAGGATGGTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGACCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATTTTGTGATGACTCAGTCTCCACTCTCCCTGCCGGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATACGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAACCCTCGTATACAGTGATTGAAACACCTACTTGAATTGGTTTCAGCAGAGGCGAGGCCAAACTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGCGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCATGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCACGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGCGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCGTACACTTTTGGACAGGGGACCAAGCTGGAGATCAAAC", "GATGTTGTGATGAAGTTTTAGTCTTAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATCCAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAAACTCCAAGGCACCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCAGTACACTTTTGGCCAGGGGACCAAGCTGGAGATAAAAC"], "naive_seq": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCATACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "duplicates": [[], [], [], [], [], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGKV2-30*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ2*01": 1.0, "IGKJ1*01": 2.5632061055214944e-20}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, true, true, true, true], "stops": [true, true, false, true, true, true, true, false, false, false, true, false, true], "codon_positions": {"v": 276, "j": 306}}, {"has_shm_indels": [true, false, true, false, true, false, false], "qr_gap_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCGCACATGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGGGACTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCT...TCAGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAACGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCGCTTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGG...CGACTGGAGATTAAAC", "", ""], "gl_gap_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTC.....TGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAG....TGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAA.GCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATC...TGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", ""], "indel_reversed_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCAGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "", ""], "unique_ids": ["3a07b6f0a9-igk", "4219142930-igk", "453132f3ab-igk", "7334912e1e-igk", "9c1dc5e656-igk", "f094dfd68a-igk", "f3509e0ef3-igk"], "invalid": false, "v_gene": "IGKV1-33*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ5*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33, 33, 33, 33, 33], "mut_freqs": [0.0, 0.0, 0.003105590062111801, 0.0, 0.0, 0.003105590062111801, 0.0], "n_mutations": [0, 0, 1, 0, 0, 1, 0], "input_seqs": ["NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCGCACATGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGGGACTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTTCAGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAACGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCGCTTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGCGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGCCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"], "naive_seq": "NNNNNNNNNNNNNNNGACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCGCTCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGKV1-33*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ5*01": 1.0}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GC", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [false, false, false, false, false, false, false], "codon_positions": {"v": 276, "j": 306}}, {"has_shm_indels": [false, true], "qr_gap_seqs": ["", "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCC...GGACCAAAGTGGATATCAAAC"], "gl_gap_seqs": ["", "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC"], "indel_reversed_seqs": ["", "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC"], "unique_ids": ["28ce45b82a-igk", "be186138e0-igk"], "invalid": false, "v_gene": "IGKV1D-13*02", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ3*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33], "mut_freqs": [0.0, 0.003105590062111801], "n_mutations": [0, 1], "input_seqs": ["NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACAATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCGGACCAAAGTGGATATCAAAC"], "naive_seq": "NNNNNNNNNNNNNNNGCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCGGTTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGKV1D-13*02": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ3*01": 1.0}, "v_3p_del": 4, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GG", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 276, "j": 306}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["28f6e090f2-igk", "b9148494e2-igk"], "invalid": false, "v_gene": "IGKV3-11*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ1*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33], "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["NNNNNNNNNNNNNNNGAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "NNNNNNNNNNNNNNNGAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC"], "naive_seq": "NNNNNNNNNNNNNNNGAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGKV3-11*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ1*01": 0.9999999999738236, "IGKJ4*01": 2.6173779204110916e-11}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "NNNNNNNNNNNNNNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 276, "j": 306}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igl.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igl.yaml new file mode 100644 index 000000000..94d3ca252 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igl.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"}}, "cyst-positions": {"IGLV2-14*04": 267, "IGLV2-23*02": 267, "IGLV1-40*01": 267}, "phen-positions": {"IGLJ1*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": -93.93319607133309, "n_clusters": 1, "n_procs": 1, "partition": [["09f5010bd3-igl", "b739ce37b7-igl", "eee6809ad6-igl"]]}], "events": [{"has_shm_indels": [false, false, true], "qr_gap_seqs": ["", "", "CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "gl_gap_seqs": ["", "", "CAGTCTGCCCTG...ACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["", "", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["09f5010bd3-igl", "b739ce37b7-igl", "eee6809ad6-igl"], "invalid": false, "v_gene": "IGLV2-23*02", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33], "mut_freqs": [0.0, 0.0, 0.0], "n_mutations": [0, 0, 0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "CAGTCTGCCCTGCTAACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTCATTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGLV2-23*02": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ1*01": 1.0}, "v_3p_del": 9, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 267, "j": 297}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-36/igk.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-36/igk.fa new file mode 100644 index 000000000..a23aed904 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-36/igk.fa @@ -0,0 +1,18 @@ +>4f03967793-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAGCGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>c2cc9da0c3-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>c0fcfe005f-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>7c67587674-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>6cf028b770-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>d1ee7f9ce6-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>6577576bb8-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>cdae60eacc-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC +>665985d2d1-igk +GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCATAAGGCGACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-36/partition-igk.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-36/partition-igk.yaml new file mode 100644 index 000000000..bdbd3a5da --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-36/partition-igk.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igk", "functionalities": {}, "seqs": {"v": {"IGKV1-33*01": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCC", "IGKV1D-13*02": "GCCATCCAGTTGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCGGGCAAGTCAGGGCATTAGCAGTGCTTTAGCCTGGTATCAGCAGAAACCAGGGAAAGCTCCTAAGCTCCTGATCTATGATGCCTCCAGTTTGGAAAGTGGGGTCCCATCAAGGTTCAGCGGCAGTGGATCTGGGACAGATTTCACTCTCACCATCAGCAGCCTGCAGCCTGAAGATTTTGCAACTTATTACTGTCAACAGTTTAATAGTTACCCTCA", "IGKV2-30*01": "GATGTTGTGATGACTCAGTCTCCACTCTCCCTGCCCGTCACCCTTGGACAGCCGGCCTCCATCTCCTGCAGGTCTAGTCAAAGCCTCGTATACAGTGATGGAAACACCTACTTGAATTGGTTTCAGCAGAGGCCAGGCCAATCTCCAAGGCGCCTAATTTATAAGGTTTCTAACCGGGACTCTGGGGTCCCAGACAGATTCAGCGGCAGTGGGTCAGGCACTGATTTCACACTGAAAATCAGCAGGGTGGAGGCTGAGGATGTTGGGGTTTATTACTGCATGCAAGGTACACACTGGCCTCC", "IGKV3-11*01": "GAAATTGTGTTGACACAGTCTCCAGCCACCCTGTCTTTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCTACTTAGCCTGGTACCAACAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGATGCATCCAACAGGGCCACTGGCATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGACTTCACTCTCACCATCAGCAGCCTAGAGCCTGAAGATTTTGCAGTTTATTACTGTCAGCAGCGTAGCAACTGGCCTCC", "IGKV3-15*01": "GAAATAGTGATGACGCAGTCTCCAGCCACCCTGTCTGTGTCTCCAGGGGAAAGAGCCACCCTCTCCTGCAGGGCCAGTCAGAGTGTTAGCAGCAACTTAGCCTGGTACCAGCAGAAACCTGGCCAGGCTCCCAGGCTCCTCATCTATGGTGCATCCACCAGGGCCACTGGTATCCCAGCCAGGTTCAGTGGCAGTGGGTCTGGGACAGAGTTCACTCTCACCATCAGCAGCCTGCAGTCTGAAGATTTTGCAGTTTATTACTGTCAGCAGTATAATAACTGGCCTCC"}, "d": {"IGKDx-x*x": "A"}, "j": {"IGKJ1*01": "GTGGACGTTCGGCCAAGGGACCAAGGTGGAAATCAAAC", "IGKJ2*01": "TGTACACTTTTGGCCAGGGGACCAAGCTGGAGATCAAAC", "IGKJ3*01": "ATTCACTTTCGGCCCTGGGACCAAAGTGGATATCAAAC", "IGKJ4*01": "GCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "IGKJ5*01": "GATCACCTTCGGCCAAGGGACACGACTGGAGATTAAAC"}}, "cyst-positions": {"IGKV1-33*01": 261, "IGKV3-11*01": 261, "IGKV1D-13*02": 261, "IGKV3-15*01": 261, "IGKV2-30*01": 276}, "phen-positions": {"IGKJ3*01": 7, "IGKJ5*01": 7, "IGKJ4*01": 7, "IGKJ2*01": 8, "IGKJ1*01": 7}}, "partitions": [{"logprob": -310.36342185147566, "n_clusters": 1, "n_procs": 1, "partition": [["4f03967793-igk", "6577576bb8-igk", "665985d2d1-igk", "6cf028b770-igk", "7c67587674-igk", "c0fcfe005f-igk", "c2cc9da0c3-igk", "cdae60eacc-igk", "d1ee7f9ce6-igk"]]}], "events": [{"has_shm_indels": [true, false, true, false, false, false, false, false, false], "qr_gap_seqs": ["GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAA....................GCGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCATAAGGCGACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "", "", "", "", ""], "gl_gap_seqs": ["GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCA.......ACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "", "", "", "", ""], "indel_reversed_seqs": ["GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTGCGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "", "", "", "", "", ""], "unique_ids": ["4f03967793-igk", "6577576bb8-igk", "665985d2d1-igk", "6cf028b770-igk", "7c67587674-igk", "c0fcfe005f-igk", "c2cc9da0c3-igk", "cdae60eacc-igk", "d1ee7f9ce6-igk"], "invalid": false, "v_gene": "IGKV1-33*01", "d_gene": "IGKDx-x*x", "j_gene": "IGKJ4*01", "cdr3_length": 36, "mature_cdr3_lengths": [36, 36, 36, 36, 36, 36, 36, 36, 36], "mut_freqs": [0.003076923076923077, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "n_mutations": [1, 0, 0, 0, 0, 0, 0, 0, 0], "input_seqs": ["GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAGCGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCATAAGGCGACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC"], "naive_seq": "GACATCCAGATGACCCAGTCTCCATCCTCCCTGTCTGCATCTGTAGGAGACAGAGTCACCATCACTTGCCAGGCGAGTCAGGACATTAGCAACTATTTAAATTGGTATCAGCAGAAACCAGGGAAAGCCCCTAAGCTCCTGATCTACGATGCATCCAATTTGGAAACAGGGGTCCCATCAAGGTTCAGTGGAAGTGGATCTGGGACAGATTTTACTTTCACCATCAGCAGCCTGCAGCCTGAAGATATTGCAACATATTACTGTCAACAGTATGATAATCTCCCTCGGCTCACTTTCGGCGGAGGGACCAAGGTGGAGATCAAAC", "duplicates": [[], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGKV1-33*01": 1.0}, "d_per_gene_support": {"IGKDx-x*x": 1.0}, "j_per_gene_support": {"IGKJ4*01": 1.0}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "G", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true], "stops": [false, false, false, false, false, false, false, false, false], "codon_positions": {"v": 261, "j": 294}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/igh.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/igh.fa new file mode 100644 index 000000000..64ad7e9bb --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/igh.fa @@ -0,0 +1,26 @@ +>3542bd38d8-igh +CCGGTCACCTTGAGGGAGTCTGGTCCCGCGCTGGTTAAACCCACACAGACCCTCACACTGACCTGCAACTTCTCTGGGCTCTCACTCAGCACTAGTGTAATGCGTGTGAGCTGGATCCGTCAGCCCCCAAGGAAGGCCCTGGAGTGGGATGCACTCATTGTTTGGGATGATCATATATACTACAGCACATCTCTGAAGACCAGGCTCACTATCTCCAAGGACACCTCCACAAACCCGGTGGTCCTTACAATGACCAACATGGTCCCTGTGGATACAGCCACGTATTACTGTGCACTGATACTCGCGAATTTGGATTTAGATTACTGGGGCCACGGAACTCTGTTCACCGTCTCCTCAA +>bc11af4843-igh +CAGGTCAGCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTGTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCAAGGGAAGGCCCTGGAGTGGCTTGCCCTCATTGATTGGGATGATCATAAATACTACAGCAGGACTGTGAAGACCAGGCTCACCATCTTCCAGTACACCTCCAGAAAACAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTATGCAGAGTCAGCTTTGATTGCTGGGGCCAGGGAAGCCTGGTCACCGTGTCCCCAG +>e6fa048856-igh +CAGGTCATCTCGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGAACTGCACCTTCTCTGGGTTCTCACTCAGCACGAGTGGAATGTGTGTGAGCTTGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTTCACTCATAGATTGGGATGATCATAAATACTACAGCAAATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACGCCCAAAAACCAGGTGGTCCTTACAATGACCAACATGTACCCTGTGGACAAAGCCACGTCTTACTGTGCACGGATACCTACTATGGTGGAATTTGAACACTGGGGCCAGGGAACCCTGGTCAGCGTCTCCTCAG +>789d880ef2-igh +CAGGTCACCTTGAGGGAGTTTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCTCACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCTCTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGGACTCATTTATTGGTATGATCATAAATAATACGGCACATCGCTGAAGAGGAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGATCCTTACAATTACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTTCACGGATACACTAAAGTGTGACTGTTGATTCCTGGGGCCAGGGAACCCTGGTCACCGTATCCTCAG +>52387a89c7-igh +CCGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCTCTCAGCACTAGTGGCATGTGTGTGAGCTGGATCCGTCAGCCCGCAGGGCAGGCCCAGGAGGGGCTTGGACTCATTGATTGGGATGTTCATAAATACTACAGCACATCTCTGAGGAACAGGCTTACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATAACCAACATGGACCCTGTGGATACAGTAACGTATTACTGTGGACGGATACCCTCAATTTTGTACCTGGATTTCTGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG +>a4b090d0be-igh +CCGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCTCTCAGCACTAGTGGCATGTGTGTGAGCTGGATCCGTCAGCCCGCAGGGCAGGCCCAGGAGGGGCTTGGACTCATTGATTGGGATGATCATAAATACTACAGCACATCTCTGAAGAACAGACTTACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGATACAGTAACGTATTACTGTGGACGGATACCCTCAATCGTGTACTTGGATTTCTGGGCCCAGGGAACCCTGGTAACCGTCTCCTCAG +>3c5f4c778a-igh +CAGGTCACCTTGAGGGCGTCTGGTCCTCCGCTGCTGAAACCCACAAAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCCCACTCAGCACGAGTGGAATGTGTGTGAGCTGGATCCTTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTCATTGGGATGCTCATAAATACTACAGCACATCTCTGAAGACCAAGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACCTGGACCCTGTGAACACAGCCACGTATTACTGTGCACGGATACTCCCAACTGTCGGTTTTGATTACTGGGGCCAGGGCACCCTGGTCACCCTCTCCTCAA +>276733008f-igh +CAGGTCACCTTGAGGGCGTCTGGTCCTGCGCTGCTGAAACCCACAAAGACCCTCACACTTACCTGCACCTTCTCTGGGTTCCCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGCGATGATCATAAATATTATACCACATCTCTTAAGACCCGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCCTACATTGACCAACATGGACCCTGTGAACACAGCCACGTATTACTGTGCACGGATACTCTCTACTATTGGTTTTGTTTACTGGGGCCAGGGTACCCTGGTCACCCTCTCCTCAG +>bb82ebe094-igh +CAGGTCACCTTGAGGGAGTTTGGTCCTGCGCTGGTGAAATCCAGACAGATCCTCACCGTGACCTGGACCTTCTCTGGGTTCTCACTCGGCACTAATGGAATGTGTGTGAGCTGGAACCGTCAGCCCCCAGGAAAGGCCATGGAGTGGCTTGGACGCATTGATTGGGATGAGCATAAATACTACAGCACATCGCTGAAAAGCAGGCTCACCATCTCCAAGGACACCTCCAAACACCGGGTGGTCCTTACAATGACCAACATGAACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTATTGATTTTAGAACTTGATTACTGGGGCTAGGGAACCCTGTTCACCGTCTCCTCAG +>7ba384a461-igh +CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGCCGAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>35fc655801-igh +CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGCCGAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>7d4166ae48-igh +CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>cfe3b29587-igh +CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCAGTGTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/igl.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/igl.fa new file mode 100644 index 000000000..e64fc7bf2 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/igl.fa @@ -0,0 +1,36 @@ +>0eb272ee70-igl +TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACAGCGGGGCAGGTTATGATGTAAACTGGTACCAGCTGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGTCCATCACAGGGCTCCAGGTAGAGGATGAGGCTGATTATTACTGCAAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>7588f09c07-igl +TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCACAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTAATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>4d37fe487e-igl +TAGTCTGTGCAGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTAGGAGCAGCTCCAACATCGGTGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCATGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGCTGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>253ca59333-igl +TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>aa25e6c0ce-igl +TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTCGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGAACCTCCGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTGCTGCCAGTCCTTTGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>8d79fca804-igl +TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCGTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCGAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>a2238f4e9a-igl +TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCGCCAAGTCTGGCACCTCGGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>b1e56e40a1-igl +TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>d5ddf0c2ec-igl +TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCGGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>ddcf0ca433-igl +TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>a3baa83300-igl +TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCGTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>b02ee7754a-igl +TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG +>20909c3943-igl +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>971ac047ee-igl +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>8807c8ff04-igl +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>14195e4958-igl +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>57537e5f22-igl +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG +>21cea6e4d0-igl +CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/partition-igh.yaml new file mode 100644 index 000000000..6573eabad --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV2-70*01": 288, "IGHV3-7*01": 285, "IGHV4-39*01": 288}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17}}, "partitions": [{"logprob": -1232.7051952670897, "n_clusters": 11, "n_procs": 1, "partition": [["276733008f-igh"], ["3542bd38d8-igh"], ["35fc655801-igh", "7ba384a461-igh"], ["3c5f4c778a-igh"], ["52387a89c7-igh"], ["789d880ef2-igh"], ["7d4166ae48-igh", "cfe3b29587-igh"], ["a4b090d0be-igh"], ["bb82ebe094-igh"], ["bc11af4843-igh"], ["e6fa048856-igh"]]}, {"logprob": -1225.333202325399, "n_clusters": 10, "n_procs": 1, "partition": [["276733008f-igh"], ["3542bd38d8-igh"], ["35fc655801-igh", "7ba384a461-igh", "7d4166ae48-igh", "cfe3b29587-igh"], ["3c5f4c778a-igh"], ["52387a89c7-igh"], ["789d880ef2-igh"], ["a4b090d0be-igh"], ["bb82ebe094-igh"], ["bc11af4843-igh"], ["e6fa048856-igh"]]}, {"logprob": -1212.234255218936, "n_clusters": 9, "n_procs": 1, "partition": [["276733008f-igh"], ["3542bd38d8-igh"], ["35fc655801-igh", "7ba384a461-igh", "7d4166ae48-igh", "cfe3b29587-igh"], ["3c5f4c778a-igh"], ["52387a89c7-igh", "bb82ebe094-igh"], ["789d880ef2-igh"], ["a4b090d0be-igh"], ["bc11af4843-igh"], ["e6fa048856-igh"]]}, {"logprob": -1198.67528973326, "n_clusters": 8, "n_procs": 1, "partition": [["276733008f-igh"], ["3542bd38d8-igh"], ["35fc655801-igh", "7ba384a461-igh", "7d4166ae48-igh", "cfe3b29587-igh"], ["3c5f4c778a-igh"], ["52387a89c7-igh", "bb82ebe094-igh"], ["789d880ef2-igh"], ["a4b090d0be-igh", "e6fa048856-igh"], ["bc11af4843-igh"]]}], "events": [{"has_shm_indels": [false, false, false, true], "qr_gap_seqs": ["", "", "", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCAGTGTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["", "", "", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATC....TCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "", "", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["35fc655801-igh", "7ba384a461-igh", "7d4166ae48-igh", "cfe3b29587-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD7-27*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39, 39, 39], "mut_freqs": [0.00558659217877095, 0.00558659217877095, 0.0, 0.0], "n_mutations": [2, 2, 0, 0], "input_seqs": ["CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGCCGAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACGCCGAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCAGTGTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCCCAACTGGGGACGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], []], "leader_seqs": ["", "", "", ""], "c_gene_seqs": ["", "", "", ""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD7-27*01": 0.9986842497443288, "IGHD1-1*01": 0.0013083916860406383, "IGHD2-8*02": 4.305929134187837e-06, "IGHD3-16*03": 2.4922276307323943e-06, "IGHD2-2*01": 3.8802168232053814e-07, "IGHD3-9*01": 1.7239118405175848e-07}, "j_per_gene_support": {"IGHJ4*02": 0.9999990472820661, "IGHJ5*02": 9.527179352372375e-07}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCC", "dj_insertion": "CG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false], "in_frames": [true, true, true, true], "stops": [false, false, false, false], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["52387a89c7-igh", "bb82ebe094-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39], "mut_freqs": [0.07541899441340782, 0.0893854748603352], "n_mutations": [27, 32], "input_seqs": ["CCGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCTCTCAGCACTAGTGGCATGTGTGTGAGCTGGATCCGTCAGCCCGCAGGGCAGGCCCAGGAGGGGCTTGGACTCATTGATTGGGATGTTCATAAATACTACAGCACATCTCTGAGGAACAGGCTTACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATAACCAACATGGACCCTGTGGATACAGTAACGTATTACTGTGGACGGATACCCTCAATTTTGTACCTGGATTTCTGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCACCTTGAGGGAGTTTGGTCCTGCGCTGGTGAAATCCAGACAGATCCTCACCGTGACCTGGACCTTCTCTGGGTTCTCACTCGGCACTAATGGAATGTGTGTGAGCTGGAACCGTCAGCCCCCAGGAAAGGCCATGGAGTGGCTTGGACGCATTGATTGGGATGAGCATAAATACTACAGCACATCGCTGAAAAGCAGGCTCACCATCTCCAAGGACACCTCCAAACACCGGGTGGTCCTTACAATGACCAACATGAACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTATTGATTTTAGAACTTGATTACTGGGGCTAGGGAACCCTGTTCACCGTCTCCTCAG"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCCTGGTTATTATACCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9987765312973691, "IGHD3-9*01": 0.0009020259961500695, "IGHD2-8*01": 0.00023352598138010188, "IGHD2-21*01": 4.480708795611879e-05, "IGHD2-15*01": 2.437252175713299e-05, "IGHD2-2*01": 1.8737115450187652e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999999740027764, "IGHJ5*02": 2.5997251241431484e-08}, "v_3p_del": 0, "d_5p_del": 18, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CC", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, true], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["a4b090d0be-igh", "e6fa048856-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-10*03", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39], "mut_freqs": [0.06983240223463687, 0.05307262569832402], "n_mutations": [25, 19], "input_seqs": ["CCGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCTCTCAGCACTAGTGGCATGTGTGTGAGCTGGATCCGTCAGCCCGCAGGGCAGGCCCAGGAGGGGCTTGGACTCATTGATTGGGATGATCATAAATACTACAGCACATCTCTGAAGAACAGACTTACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGATACAGTAACGTATTACTGTGGACGGATACCCTCAATCGTGTACTTGGATTTCTGGGCCCAGGGAACCCTGGTAACCGTCTCCTCAG", "CAGGTCATCTCGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGAACTGCACCTTCTCTGGGTTCTCACTCAGCACGAGTGGAATGTGTGTGAGCTTGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTTCACTCATAGATTGGGATGATCATAAATACTACAGCAAATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACGCCCAAAAACCAGGTGGTCCTTACAATGACCAACATGTACCCTGTGGACAAAGCCACGTCTTACTGTGCACGGATACCTACTATGGTGGAATTTGAACACTGGGGCCAGGGAACCCTGGTCAGCGTCTCCTCAG"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACCTACTATGGTGTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-10*03": 0.8607442180179671, "IGHD2-8*01": 0.11314377836256438, "IGHD1-26*01": 0.012391978706903718, "IGHD3-16*03": 0.005675776514860024, "IGHD2-2*01": 0.005231198365534917, "IGHD6-6*01": 0.0020015610173958285, "IGHD2-21*01": 0.0004353714887649871, "IGHD2-15*01": 0.00037611752603844027}, "j_per_gene_support": {"IGHJ4*02": 0.9999999120282478, "IGHJ5*02": 8.797175077085633e-08}, "v_3p_del": 0, "d_5p_del": 4, "d_3p_del": 18, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "C", "dj_insertion": "G", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["276733008f-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD2-8*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.05865921787709497], "n_mutations": [21], "input_seqs": ["CAGGTCACCTTGAGGGCGTCTGGTCCTGCGCTGCTGAAACCCACAAAGACCCTCACACTTACCTGCACCTTCTCTGGGTTCCCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGCGATGATCATAAATATTATACCACATCTCTTAAGACCCGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCCTACATTGACCAACATGGACCCTGTGAACACAGCCACGTATTACTGTGCACGGATACTCTCTACTATTGGTTTTGTTTACTGGGGCCAGGGTACCCTGGTCACCCTCTCCTCAG"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTCTGTACTAATGGTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD2-8*01": 0.9461862037204629, "IGHD1-26*01": 0.030888698799681313, "IGHD2-8*02": 0.013695925534625229, "IGHD1-1*01": 0.0070928013998329455, "IGHD3-10*03": 0.0021363705454102645}, "j_per_gene_support": {"IGHJ4*02": 0.9999213816654228, "IGHJ5*02": 7.861833457443879e-05}, "v_3p_del": 0, "d_5p_del": 7, "d_3p_del": 12, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["3542bd38d8-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.08100558659217877], "n_mutations": [29], "input_seqs": ["CCGGTCACCTTGAGGGAGTCTGGTCCCGCGCTGGTTAAACCCACACAGACCCTCACACTGACCTGCAACTTCTCTGGGCTCTCACTCAGCACTAGTGTAATGCGTGTGAGCTGGATCCGTCAGCCCCCAAGGAAGGCCCTGGAGTGGGATGCACTCATTGTTTGGGATGATCATATATACTACAGCACATCTCTGAAGACCAGGCTCACTATCTCCAAGGACACCTCCACAAACCCGGTGGTCCTTACAATGACCAACATGGTCCCTGTGGATACAGCCACGTATTACTGTGCACTGATACTCGCGAATTTGGATTTAGATTACTGGGGCCACGGAACTCTGTTCACCGTCTCCTCAA"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTCGCGATTTTTGGAGTAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9902763725121576, "IGHD3-16*03": 0.008544451016388389, "IGHD1-1*01": 0.0007247982551016534, "IGHD3-9*01": 0.0003496191248750958, "IGHD2-15*01": 0.00010475909149021817}, "j_per_gene_support": {"IGHJ4*02": 0.9994642028610878, "IGHJ5*02": 0.0005357971389022287}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 12, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCG", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["3c5f4c778a-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD1-1*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.04748603351955307], "n_mutations": [17], "input_seqs": ["CAGGTCACCTTGAGGGCGTCTGGTCCTCCGCTGCTGAAACCCACAAAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCCCACTCAGCACGAGTGGAATGTGTGTGAGCTGGATCCTTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTCATTGGGATGCTCATAAATACTACAGCACATCTCTGAAGACCAAGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACCTGGACCCTGTGAACACAGCCACGTATTACTGTGCACGGATACTCCCAACTGTCGGTTTTGATTACTGGGGCCAGGGCACCCTGGTCACCCTCTCCTCAA"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTCCCAACTGTCGGTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD1-1*01": 0.517891281008128, "IGHD7-27*01": 0.46191566817742113, "IGHD2-2*01": 0.012422735949157162, "IGHD2-8*02": 0.007703350299090547, "IGHD3-9*01": 6.696456621221164e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999971915780251, "IGHJ5*02": 2.808421971259051e-06}, "v_3p_del": 0, "d_5p_del": 4, "d_3p_del": 7, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCC", "dj_insertion": "TCGGT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["789d880ef2-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD3-9*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.061452513966480445], "n_mutations": [22], "input_seqs": ["CAGGTCACCTTGAGGGAGTTTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCTCACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCTCTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGGACTCATTTATTGGTATGATCATAAATAATACGGCACATCGCTGAAGAGGAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGATCCTTACAATTACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTTCACGGATACACTAAAGTGTGACTGTTGATTCCTGGGGCCAGGGAACCCTGGTCACCGTATCCTCAG"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACACGATATTTTGACTGTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD3-9*01": 0.8499003721779994, "IGHD1-26*01": 0.10106714858525212, "IGHD2-8*01": 0.02529728640881477, "IGHD6-19*01": 0.023363293418709654, "IGHD2-21*01": 0.00037189940922378195}, "j_per_gene_support": {"IGHJ4*02": 0.9994816824392659, "IGHJ5*02": 0.0005183175607342217}, "v_3p_del": 0, "d_5p_del": 5, "d_3p_del": 11, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "codon_positions": {"v": 288, "j": 324}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["bc11af4843-igh"], "invalid": false, "v_gene": "IGHV2-70*01", "d_gene": "IGHD2-2*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.055865921787709494], "n_mutations": [20], "input_seqs": ["CAGGTCAGCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTGTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCAAGGGAAGGCCCTGGAGTGGCTTGCCCTCATTGATTGGGATGATCATAAATACTACAGCAGGACTGTGAAGACCAGGCTCACCATCTTCCAGTACACCTCCAGAAAACAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTATGCAGAGTCAGCTTTGATTGCTGGGGCCAGGGAAGCCTGGTCACCGTGTCCCCAG"], "naive_seq": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATACTATGCCGAGTCAGCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70*01": 1.0}, "d_per_gene_support": {"IGHD2-2*01": 0.5930148960805628, "IGHD2-8*01": 0.22296426646393663, "IGHD2-8*02": 0.14448352952763707, "IGHD3-16*03": 0.023934849107146286, "IGHD3-10*03": 0.0156024588207227}, "j_per_gene_support": {"IGHJ4*02": 0.9999806387199804, "IGHJ5*02": 1.9361280021906524e-05}, "v_3p_del": 0, "d_5p_del": 25, "d_3p_del": 0, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GAGTCAG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 324}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/partition-igl.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/partition-igl.yaml new file mode 100644 index 000000000..ed0243dfb --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-39/partition-igl.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igl", "functionalities": {}, "seqs": {"v": {"IGLV1-40*01": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTC", "IGLV2-14*04": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTC", "IGLV2-23*02": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGATGTTGGGAGTTATAACCTTGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGAGGTCAGTAAGCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACAATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCTGCTCATATGCAGGTAGTAGCACTTTC"}, "d": {"IGLDx-x*x": "A"}, "j": {"IGLJ1*01": "TTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "IGLJ3*02": "TTGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"}}, "cyst-positions": {"IGLV2-14*04": 267, "IGLV2-23*02": 267, "IGLV1-40*01": 267}, "phen-positions": {"IGLJ1*01": 7, "IGLJ3*02": 7}}, "partitions": [{"logprob": -926.1014724016392, "n_clusters": 2, "n_procs": 1, "partition": [["0eb272ee70-igl", "253ca59333-igl", "4d37fe487e-igl", "7588f09c07-igl", "8d79fca804-igl", "a2238f4e9a-igl", "a3baa83300-igl", "aa25e6c0ce-igl", "b02ee7754a-igl", "b1e56e40a1-igl", "d5ddf0c2ec-igl", "ddcf0ca433-igl"], ["14195e4958-igl", "20909c3943-igl", "21cea6e4d0-igl", "57537e5f22-igl", "8807c8ff04-igl", "971ac047ee-igl"]]}], "events": [{"has_shm_indels": [false, false, false, false, false, false, false, false, false, false, false, true], "qr_gap_seqs": ["", "", "", "", "", "", "", "", "", "", "", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGAT........TCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "gl_gap_seqs": ["", "", "", "", "", "", "", "", "", "", "", "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", "", "", "", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "unique_ids": ["0eb272ee70-igl", "253ca59333-igl", "4d37fe487e-igl", "7588f09c07-igl", "8d79fca804-igl", "a2238f4e9a-igl", "a3baa83300-igl", "aa25e6c0ce-igl", "b02ee7754a-igl", "b1e56e40a1-igl", "d5ddf0c2ec-igl", "ddcf0ca433-igl"], "invalid": false, "v_gene": "IGLV1-40*01", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ1*01", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39], "mut_freqs": [0.029940119760479042, 0.014970059880239521, 0.03293413173652695, 0.023952095808383235, 0.029940119760479042, 0.020958083832335328, 0.02694610778443114, 0.029940119760479042, 0.023952095808383235, 0.023952095808383235, 0.023952095808383235, 0.020958083832335328], "n_mutations": [10, 5, 11, 8, 10, 7, 9, 10, 8, 8, 8, 7], "input_seqs": ["TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACAGCGGGGCAGGTTATGATGTAAACTGGTACCAGCTGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGTCCATCACAGGGCTCCAGGTAGAGGATGAGGCTGATTATTACTGCAAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCAGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTAGGAGCAGCTCCAACATCGGTGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCATGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGCTGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCACAAACTCCTCATCTATGGTAACAGCAATAGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTAATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCGTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCGAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCGCCAAGTCTGGCACCTCGGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCGTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTCGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGTCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGAACCTCCGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTGCTGCCAGTCCTTTGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCGGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGCACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGACCATCACAGGGCTCCAGGCGGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTTAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "TAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCCGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTAAACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACAGGGCTCCAGGCAGAGGATGAGGCTGATTATTTCTGCCAGTCCTATTACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG"], "naive_seq": "CAGTCTGTGCTGACGCAGCCGCCCTCAGTGTCTGGGGCCCCAGGGCAGAGGGTCACCATCTCCTGCACTGGGAGCAGCTCCAACATCGGGGCAGGTTATGATGTACACTGGTACCAGCAGCTTCCAGGAACAGCCCCCAAACTCCTCATCTATGGTAACAGCAATCGGCCCTCAGGGGTCCCTGACCGATTCTCTGGCTCCAAGTCTGGCACCTCAGCCTCCCTGGCCATCACTGGGCTCCAGGCTGAGGATGAGGCTGATTATTACTGCCAGTCCTATGACAGCAGCCTGAGTGGTTATGTCTTCGGAACTGGGACCAAGGTCACCGTCCTAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGLV1-40*01": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ1*01": 1.0}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, true, true, true], "stops": [true, true, true, true, true, true, true, true, true, true, true, true], "codon_positions": {"v": 267, "j": 303}}, {"has_shm_indels": [true, false, false, false, false, true], "qr_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", "", "", "", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "gl_gap_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCA........GCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", "", "", "", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATC.GCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "indel_reversed_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "", "", "", "", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "unique_ids": ["14195e4958-igl", "20909c3943-igl", "21cea6e4d0-igl", "57537e5f22-igl", "8807c8ff04-igl", "971ac047ee-igl"], "invalid": false, "v_gene": "IGLV2-14*04", "d_gene": "IGLDx-x*x", "j_gene": "IGLJ3*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39, 39, 39, 39, 39], "mut_freqs": [0.0, 0.0, 0.0, 0.0, 0.0, 0.0], "n_mutations": [0, 0, 0, 0, 0, 0], "input_seqs": ["CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAACAAGTCTGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG"], "naive_seq": "CAGTCTGCCCTGACTCAGCCTGCCTCCGTGTCTGGGTCTCCTGGACAGTCGATCACCATCTCCTGCACTGGAACCAGCAGTGACGTTGGTGGTTATAACTATGTCTCCTGGTACCAACAGCACCCAGGCAAAGCCCCCAAACTCATGATTTATGATGTCAGTAATCGGCCCTCAGGGGTTTCTAATCGCTTCTCTGGCTCCAAGTCTGGCAACACGGCCTCCCTGACCATCTCTGGGCTCCAGGCTGAGGACGAGGCTGATTATTACTGCAGCTCATATACAAGCAGCAGCACTCTCAGGGTGTTCGGCGGAGGGACCAAGCTGACCGTCCTAG", "duplicates": [[], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", ""], "v_per_gene_support": {"IGLV2-14*04": 1.0}, "d_per_gene_support": {"IGLDx-x*x": 1.0}, "j_per_gene_support": {"IGLJ3*02": 1.0}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "A", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true], "stops": [false, false, false, false, false, false], "codon_positions": {"v": 267, "j": 303}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-48/igh.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-48/igh.fa new file mode 100644 index 000000000..7e6c3e4d3 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-48/igh.fa @@ -0,0 +1,24 @@ +>be186138e0-igh +CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGCGTATAGTGGGAGCTACTACTTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>28ce45b82a-igh +CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGCGTATAGTGGGAGCTACTACTTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>b739ce37b7-igh +CAGGTCCAGCTGATGCAGTCTTGGGCTGAGCTGAAGAAGCCTGTGTCCTCGCTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTAAGATATCAACTGTGTGCGACAGGCCCCTGGACAGGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACATCGCACAGAAGTTCCACGGCAGAGTCACGATTCCCGTGGAAATATACACGATGACAGCCTACATGGAGCTGAGCAGCATGAGATCCGGGGACACGGCCGTGTATTACTGTGGGAGATGACGGGAGGGAGATGGTGTTGATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTCTTCTCAC +>eee6809ad6-igh +CAGGTCGAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGCCTGGGGCCTCGCTGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCTGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTTGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGCTAAGCAGCCTGAGATCCGAGGACACGGTCGTGTATAACTGTGAGAGCCGCAACACGTTATATCATAAAACTAACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTCCTCAG +>09f5010bd3-igh +CAGGTCCAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGCTGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTAGGGAGGTCAGGTAGGAGTGGATGGGAAGGATCATCCCTATCCGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTGGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGGTAAGCAGCCTTAGATCCGAGGACACGCTCGTGTATTACTGTGAGAGCCACCACGAGTTATGTCATAAAAATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTGCTCAG +>cb8a759f1a-igh +GAGGTGCAACTGGTGGCGTCTGGGGGAGGCTTGGACCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGCATTCACCTTTAGTTGCTATCGAATTCGCTGGGTCCGCCAGACTCAAGGGAAGGGGCTTGGCTAACATAAAGCAAGATGCAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGTAAATGAACAGCCTGAGAGCCGAGGGCACGGCTGTGTCTTACTGTGCGCGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCTGCGAACCCTGGTCACCGTCTCCTCAG +>14195e4958-igh +TTGGTGCAGCTGGTGGAGTCTGGGAGTGTATGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGGCTCTCATGGGCAGCCTCTGGATTCACCTTTACTAGCTATTTGATGAGCTGGGTTGGCCAGGCTCCAGGGAAGGGGCTGGAGTGCGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACTACTCTCCAGAGACAACGCCAAGAACTCACTGTATGTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGTCCATCCCCTGGTGGTCCTGTGTGGGGTGACTACTGGGGCCAGGGAATCCTGGTCACCGTCTCCTCAG +>e11acbe3ab-igh +TAGGTGCAGCCGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTACTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGTGGCTGGAGTGTGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCAGCTCCAGAGACAACACCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACCCGGCTGTGTATTACTGTGCGAGAGACCAATCTGCTAGTGGTCTTGGGCGGGGTGACTACTGGGGCCAGGGAAGCCTGGTCACCGTCTCCTCAG +>eee2c7797d-igh +TAGGTGCAGCGGGTGGAGTATGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGAGCAGCCTCTGGATTCACCTTTACTAGCTATTGGATGAGCTGGGTCGGCCAGGCTCCAGGGAAGGGGCTGGAGTGTGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGCACTCTGTGAAGGGCCGACTCACCAGCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAATTGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGCAACCGGCTAGTGGTGTTTGGCGGGCTGAATACTGGGGCCAGGGAAGCCTGGTCACCGTCTCCTCAG +>57537e5f22-igh +TAGGTGCAGCTTGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCATGTGCAGCCTCTCGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGGTCCAGGGAAGGGGCTGGAGTGGGTGGCCGAGATAAAGCAAGATGGTAGTCAGAAATACTATCTGGACTCACTGAAGGGCCGATTCACCAACTCCAGAGACAACGCCAAGACCTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGGGGTCCCGCCATTGCAACTGACACCGGTGACTACTGGGGCCAGGCAATCCTGGGCACCGTCTCCTCAG +>21cea6e4d0-igh +TAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGTTCCCTGAGACTCTCCTGTGCAACCTCTGGATTCACCTTTAGTAGCTATTGATGAGCAGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAATGGTTGGCCAACATAAAGTAAGATGGAAGTGAGAAATACTATCTGGACTCTGTGAAGGGCCGACTTACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGAATTCCGCTAGTGGACCTGTTATCGGTGACTCCTGGGGCCAGGGATTCCTGGTCTCCGTCTCCTCAG +>8b9ef6b10e-igh +TAGCTGCAGCTGGCGGAGTCTGGGGGAGGCTTGGTCGAGTCTGGGGGGTCCATGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGTTTTTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATTAAGCAAGATGGAAGTGAGAAATTCTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTAACTGTATCTGCAAATGAACACCCTGAAAGCCGAGGACACGGCTGTGTATTATTGTGCGAGAGAGCGTTCAGCTCGGGGACATGAGCGGGCTGACTAGTGGGGCCAGGGAATCCTTGTCACCGTCTCCACAG diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-48/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-48/partition-igh.yaml new file mode 100644 index 000000000..5633fec7a --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-48/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV2-70*01": 288, "IGHV3-7*01": 285, "IGHV4-39*01": 288}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17}}, "partitions": [{"logprob": -1544.4545167918438, "n_clusters": 11, "n_procs": 1, "partition": [["09f5010bd3-igh"], ["14195e4958-igh"], ["21cea6e4d0-igh"], ["28ce45b82a-igh", "be186138e0-igh"], ["57537e5f22-igh"], ["8b9ef6b10e-igh"], ["b739ce37b7-igh"], ["cb8a759f1a-igh"], ["e11acbe3ab-igh"], ["eee2c7797d-igh"], ["eee6809ad6-igh"]]}, {"logprob": -1516.7755376801156, "n_clusters": 10, "n_procs": 1, "partition": [["09f5010bd3-igh"], ["14195e4958-igh"], ["21cea6e4d0-igh"], ["28ce45b82a-igh", "be186138e0-igh"], ["57537e5f22-igh"], ["8b9ef6b10e-igh"], ["b739ce37b7-igh"], ["cb8a759f1a-igh"], ["e11acbe3ab-igh", "eee2c7797d-igh"], ["eee6809ad6-igh"]]}, {"logprob": -1490.1343121177315, "n_clusters": 9, "n_procs": 1, "partition": [["09f5010bd3-igh", "eee6809ad6-igh"], ["14195e4958-igh"], ["21cea6e4d0-igh"], ["28ce45b82a-igh", "be186138e0-igh"], ["57537e5f22-igh"], ["8b9ef6b10e-igh"], ["b739ce37b7-igh"], ["cb8a759f1a-igh"], ["e11acbe3ab-igh", "eee2c7797d-igh"]]}, {"logprob": -1469.2617278269597, "n_clusters": 8, "n_procs": 1, "partition": [["09f5010bd3-igh", "eee6809ad6-igh"], ["14195e4958-igh"], ["21cea6e4d0-igh", "57537e5f22-igh"], ["28ce45b82a-igh", "be186138e0-igh"], ["8b9ef6b10e-igh"], ["b739ce37b7-igh"], ["cb8a759f1a-igh"], ["e11acbe3ab-igh", "eee2c7797d-igh"]]}, {"logprob": -1452.7244848267685, "n_clusters": 7, "n_procs": 1, "partition": [["09f5010bd3-igh", "eee6809ad6-igh"], ["14195e4958-igh"], ["21cea6e4d0-igh", "57537e5f22-igh"], ["28ce45b82a-igh", "be186138e0-igh"], ["8b9ef6b10e-igh", "e11acbe3ab-igh", "eee2c7797d-igh"], ["b739ce37b7-igh"], ["cb8a759f1a-igh"]]}, {"logprob": -1435.1404015214432, "n_clusters": 6, "n_procs": 1, "partition": [["09f5010bd3-igh", "eee6809ad6-igh"], ["14195e4958-igh", "8b9ef6b10e-igh", "e11acbe3ab-igh", "eee2c7797d-igh"], ["21cea6e4d0-igh", "57537e5f22-igh"], ["28ce45b82a-igh", "be186138e0-igh"], ["b739ce37b7-igh"], ["cb8a759f1a-igh"]]}], "events": [{"has_shm_indels": [true, false, false, false], "qr_gap_seqs": ["TTGGTGCAGCTGGTGGAGTCTGGGAGTGTATGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGGCTCTCATGGGCAGCCTCTGGATTCACCTTTACTAGCTATTTGATGAGCTGGGTTGGCCAGGCTCCAGGGAAGGGGCTGGAGTGCGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACTACTCTCCAGAGACAACGCCAAGAACTCACTGTATGTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGTCCATCCCCTGGTGGTCCTGTGTGGGGTGACTACTGGGGCCAGGGAATCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["GAGGTGCAGCTGGTGGAGTCTGG........GGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCA.TCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGCCTTCAGCTCGTGGTCCTGTGCGGGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["TTGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGGCTCTCATGGGCAGCCTCTGGATTCACCTTTACTAGCTATTTGATGAGCTGGGTTGGCCAGGCTCCAGGGAAGGGGCTGGAGTGCGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACTATCTCCAGAGACAACGCCAAGAACTCACTGTATGTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGTCCATCCCCTGGTGGTCCTGTGTGGGGTGACTACTGGGGCCAGGGAATCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["14195e4958-igh", "8b9ef6b10e-igh", "e11acbe3ab-igh", "eee2c7797d-igh"], "invalid": false, "v_gene": "IGHV3-7*01", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48, 48, 48, 48], "mut_freqs": [0.06318681318681318, 0.07417582417582418, 0.04395604395604396, 0.057692307692307696], "n_mutations": [23, 27, 16, 21], "input_seqs": ["TTGGTGCAGCTGGTGGAGTCTGGGAGTGTATGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGGCTCTCATGGGCAGCCTCTGGATTCACCTTTACTAGCTATTTGATGAGCTGGGTTGGCCAGGCTCCAGGGAAGGGGCTGGAGTGCGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACTACTCTCCAGAGACAACGCCAAGAACTCACTGTATGTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGTCCATCCCCTGGTGGTCCTGTGTGGGGTGACTACTGGGGCCAGGGAATCCTGGTCACCGTCTCCTCAG", "TAGCTGCAGCTGGCGGAGTCTGGGGGAGGCTTGGTCGAGTCTGGGGGGTCCATGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGTTTTTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATTAAGCAAGATGGAAGTGAGAAATTCTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTAACTGTATCTGCAAATGAACACCCTGAAAGCCGAGGACACGGCTGTGTATTATTGTGCGAGAGAGCGTTCAGCTCGGGGACATGAGCGGGCTGACTAGTGGGGCCAGGGAATCCTTGTCACCGTCTCCACAG", "TAGGTGCAGCCGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTACTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGTGGCTGGAGTGTGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCAGCTCCAGAGACAACACCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACCCGGCTGTGTATTACTGTGCGAGAGACCAATCTGCTAGTGGTCTTGGGCGGGGTGACTACTGGGGCCAGGGAAGCCTGGTCACCGTCTCCTCAG", "TAGGTGCAGCGGGTGGAGTATGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGAGCAGCCTCTGGATTCACCTTTACTAGCTATTGGATGAGCTGGGTCGGCCAGGCTCCAGGGAAGGGGCTGGAGTGTGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGCACTCTGTGAAGGGCCGACTCACCAGCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAATTGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGCAACCGGCTAGTGGTGTTTGGCGGGCTGAATACTGGGGCCAGGGAAGCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGACCCTCCAGCTCGTGGTGCTGGGCGGGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], []], "leader_seqs": ["", "", "", ""], "c_gene_seqs": ["", "", "", ""], "v_per_gene_support": {"IGHV3-7*01": 1.0}, "d_per_gene_support": {"IGHD6-6*01": 0.8827811499304686, "IGHD2-8*02": 0.06315167177721374, "IGHD2-15*01": 0.030253089804588285, "IGHD2-2*01": 0.016670827265915837, "IGHD3-16*03": 0.002242430498400677, "IGHD2-21*01": 0.002201687961850952, "IGHD7-27*01": 0.001563147351145642, "IGHD1-14*01": 0.000716105570227255, "IGHD2-8*01": 0.000195851868502408, "IGHD3-10*03": 0.00019440052653640238, "IGHD1-26*01": 2.9637445145535326e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999934833721534, "IGHJ5*02": 6.516627850595669e-06}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 2, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCTC", "dj_insertion": "GGTGCTGGGCGGGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false], "in_frames": [true, true, true, true], "stops": [false, true, true, true], "codon_positions": {"v": 285, "j": 330}}, {"has_shm_indels": [true, false], "qr_gap_seqs": ["CAGGTCCAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGC............TGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTAGGGAGGTCAGGTAGGAGTGGATGGGAAGGATCATCCCTATCCGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTGGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGGTAAGCAGCCTTAGATCCGAGGACACGCTCGTGTATTACTGTGAGAGCCACCACGAGTTATGTCATAAAAATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTGCTCAG", ""], "gl_gap_seqs": ["CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTT...............GAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGCCGCCACGCGTTATACCATAAAACTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", ""], "indel_reversed_seqs": ["CAGGTCCAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGCCTGGGTCCTCGGTGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTGGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGGTAAGCAGCCTTAGATCCGAGGACACGCTCGTGTATTACTGTGAGAGCCACCACGAGTTATGTCATAAAAATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTGCTCAG", ""], "unique_ids": ["09f5010bd3-igh", "eee6809ad6-igh"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD3-16*03", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48, 48], "mut_freqs": [0.09065934065934066, 0.09065934065934066], "n_mutations": [33, 33], "input_seqs": ["CAGGTCCAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGCTGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTAGGGAGGTCAGGTAGGAGTGGATGGGAAGGATCATCCCTATCCGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTGGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGGTAAGCAGCCTTAGATCCGAGGACACGCTCGTGTATTACTGTGAGAGCCACCACGAGTTATGTCATAAAAATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTGCTCAG", "CAGGTCGAGCTGCTGCAGCCTGGGGCTGAGCTGAAGAAGCCTGGGGCCTCGCTGCAGGTCTCCTGCAAGGCTTCTGGAGGCACGTTCAGCAGCTTTGCTATCAACTGGGTGAGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCTGTGGTATAGCAAACTTCGCACAGAAGTTTCAGGGTTGAGTCACGATTCCCGCGGAAAAATCCACGATGCCAGCCTACATGGAGCTAAGCAGCCTGAGATCCGAGGACACGGTCGTGTATAACTGTGAGAGCCGCAACACGTTATATCATAAAACTAACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTTTCCTCAG"], "naive_seq": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGCCGCCACGCGTTATACCATAAAACTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD3-16*03": 0.4900777076508471, "IGHD1-14*01": 0.4311215054514137, "IGHD3-3*01": 0.06508791962597235, "IGHD2-2*01": 0.006632268918067831, "IGHD3-10*03": 0.005661415592202817, "IGHD2-8*01": 0.0008411981499737442, "IGHD3-9*01": 0.0005779846114654471}, "j_per_gene_support": {"IGHJ4*02": 0.9999999999926672, "IGHJ5*02": 7.306826995028274e-12}, "v_3p_del": 3, "d_5p_del": 28, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGCCACG", "dj_insertion": "ATAAAACT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [true, true], "codon_positions": {"v": 285, "j": 330}}, {"has_shm_indels": [true, false], "qr_gap_seqs": ["TAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGTTCCCTGAGACTCTCCTGTGCAACCTCTGGATTCACCTTTAGTAGCTATT.GATGAGCAGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAATGGTTGGCCAACATAAAGTAAGATGGAAGTGAGAAATACTATCTGGACTCTGTGAAGGGCCGACTTACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGAATTCCGCTAGTGGACCTGTTATCGGTGACTCCTGGGGCCAGGGATTCCTGGTCTCCGTCTCCTCAG", ""], "gl_gap_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGGTCCCGCCAGTGCACCTGATACCGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", ""], "indel_reversed_seqs": ["TAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGTTCCCTGAGACTCTCCTGTGCAACCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCAGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAATGGTTGGCCAACATAAAGTAAGATGGAAGTGAGAAATACTATCTGGACTCTGTGAAGGGCCGACTTACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGAATTCCGCTAGTGGACCTGTTATCGGTGACTCCTGGGGCCAGGGATTCCTGGTCTCCGTCTCCTCAG", ""], "unique_ids": ["21cea6e4d0-igh", "57537e5f22-igh"], "invalid": false, "v_gene": "IGHV3-7*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48, 48], "mut_freqs": [0.06593406593406594, 0.06318681318681318], "n_mutations": [24, 23], "input_seqs": ["TAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGTTCCCTGAGACTCTCCTGTGCAACCTCTGGATTCACCTTTAGTAGCTATTGATGAGCAGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAATGGTTGGCCAACATAAAGTAAGATGGAAGTGAGAAATACTATCTGGACTCTGTGAAGGGCCGACTTACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGAATTCCGCTAGTGGACCTGTTATCGGTGACTCCTGGGGCCAGGGATTCCTGGTCTCCGTCTCCTCAG", "TAGGTGCAGCTTGTGGAGTCTGGAGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCATGTGCAGCCTCTCGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGGTCCAGGGAAGGGGCTGGAGTGGGTGGCCGAGATAAAGCAAGATGGTAGTCAGAAATACTATCTGGACTCACTGAAGGGCCGATTCACCAACTCCAGAGACAACGCCAAGACCTCACTGTATCTGCAAATGAGCAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGGGGGTCCCGCCATTGCAACTGACACCGGTGACTACTGGGGCCAGGCAATCCTGGGCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGGTCCCGCCAGTGCACCTGATACCGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-7*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.5227152042607583, "IGHD3-16*03": 0.23763735026646135, "IGHD1-1*01": 0.21547281933764997, "IGHD1-14*01": 0.00955211669343816, "IGHD6-6*01": 0.008037545682559977, "IGHD7-27*01": 0.004264354294965131, "IGHD2-15*01": 0.0012297043482626727, "IGHD2-21*01": 0.0010880333202834625, "IGHD1-26*01": 2.100946699030204e-06, "IGHD3-9*01": 7.708488661446781e-07}, "j_per_gene_support": {"IGHJ4*02": 0.9999914368424356, "IGHJ5*02": 8.563157549740184e-06}, "v_3p_del": 0, "d_5p_del": 26, "d_3p_del": 0, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGGTCCCGCCAGTGCACCTG", "dj_insertion": "GG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [false, true], "stops": [true, true], "codon_positions": {"v": 285, "j": 330}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["28ce45b82a-igh", "be186138e0-igh"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48, 48], "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGCGTATAGTGGGAGCTACTACTTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGCGTATAGTGGGAGCTACTACTTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGGCGTATAGTGGGAGCTACTACTTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD1-26*01": 0.9999999999994387, "IGHD2-15*01": 5.621796129949252e-13}, "j_per_gene_support": {"IGHJ4*02": 0.9999999998758256, "IGHJ5*02": 1.2417242399287063e-10}, "v_3p_del": 3, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GC", "dj_insertion": "TT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 285, "j": 330}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["b739ce37b7-igh"], "invalid": false, "v_gene": "IGHV1-69*04", "d_gene": "IGHD2-21*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.07692307692307693], "n_mutations": [28], "input_seqs": ["CAGGTCCAGCTGATGCAGTCTTGGGCTGAGCTGAAGAAGCCTGTGTCCTCGCTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTAAGATATCAACTGTGTGCGACAGGCCCCTGGACAGGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACATCGCACAGAAGTTCCACGGCAGAGTCACGATTCCCGTGGAAATATACACGATGACAGCCTACATGGAGCTGAGCAGCATGAGATCCGGGGACACGGCCGTGTATTACTGTGGGAGATGACGGGAGGGAGATGGTGTTGATTACTTTGACTATTGGGGCCAGGGAACCCTGGTCACCGTCTTCTCAC"], "naive_seq": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGATGACGGGAGGGAGATGGTGGTGATTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-69*04": 1.0}, "d_per_gene_support": {"IGHD2-21*01": 0.8236902394964637, "IGHD2-8*02": 0.09639164582468808, "IGHD1-26*01": 0.050222269119530816, "IGHD3-10*03": 0.018545432573660786, "IGHD2-8*01": 0.011150412985645676}, "j_per_gene_support": {"IGHJ4*02": 0.9999999532874437, "IGHJ5*02": 4.671254649868613e-08}, "v_3p_del": 2, "d_5p_del": 9, "d_3p_del": 9, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TGACGGGAGGGAGA", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "codon_positions": {"v": 285, "j": 330}}, {"has_shm_indels": [true], "qr_gap_seqs": ["GAGGTGCAACTGGTGGCGTCTGGGGGAGGCTTGGACCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGCATTCACCTTTAGTTGCTATCGAATTCGCTGGGTCCGCCAGACTCAAGGGAAGGGGCT........TGGCTAACATAAAGCAAGATGCAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGTAAATGAACAGCCTGAGAGCCGAGGGCACGGCTGTGTCTTACTGTGCGCGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCTGCGAACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["GAGGTGCAACTGGTGGCGTCTGGGGGAGGCTTGGACCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGCATTCACCTTTAGTTGCTATCGAATTCGCTGGGTCCGCCAGACTCAAGGGAAGGGGCTGGAGTGGGTGGCTAACATAAAGCAAGATGCAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGTAAATGAACAGCCTGAGAGCCGAGGGCACGGCTGTGTCTTACTGTGCGCGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCTGCGAACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["cb8a759f1a-igh"], "invalid": false, "v_gene": "IGHV3-7*01", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.0521978021978022], "n_mutations": [19], "input_seqs": ["GAGGTGCAACTGGTGGCGTCTGGGGGAGGCTTGGACCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGCATTCACCTTTAGTTGCTATCGAATTCGCTGGGTCCGCCAGACTCAAGGGAAGGGGCTTGGCTAACATAAAGCAAGATGCAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGTAAATGAACAGCCTGAGAGCCGAGGGCACGGCTGTGTCTTACTGTGCGCGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCTGCGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGTACATTGCCCGAGTGCACGCGTCCGCGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-7*01": 1.0}, "d_per_gene_support": {"IGHD6-6*01": 0.8490602405645918, "IGHD3-16*03": 0.07978369326487597, "IGHD3-3*01": 0.03873207772642884, "IGHD1-1*01": 0.021785598637224474, "IGHD2-21*01": 0.010638389806893623}, "j_per_gene_support": {"IGHJ4*02": 0.9998907137850829, "IGHJ5*02": 0.00010928621492536946}, "v_3p_del": 1, "d_5p_del": 13, "d_3p_del": 0, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TACATTGCCCGAGTGCACG", "dj_insertion": "GCGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "codon_positions": {"v": 285, "j": 330}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-54/igh.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-54/igh.fa new file mode 100644 index 000000000..f9871c0c1 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-54/igh.fa @@ -0,0 +1,12 @@ +>b997fa9304-igh +CTGGTTCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGAATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATCTGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGACACAGGAACCACGAGTTCGCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG +>f3509e0ef3-igh +CTAGTTCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGAATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATCTGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGACACAGGAACCACGAGTTTGCTACGATATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG +>453132f3ab-igh +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACCCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGTCATGGACTGGGTCCGCCAGGCACCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAACAGGCAGCGGAACCAGAACTTTCCTACGGTATAGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG +>f094dfd68a-igh +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGGTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGGAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGTCACGGCTGTGGATTACTGTGCGAGAGGGCCGGCACCGGAACCGCTACTTACCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGGCACCGTCTCCTCAG +>3a07b6f0a9-igh +CAGGTGCAGCTGGTGGAATCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTGCTGTGCAGCGTCTGGATTCACCTTCAGTAGGTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGAGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGTTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGCCGGAACCGGAACAAATAGTTGCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG +>7334912e1e-igh +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTCTCCTTTTCAGCGTCTGGATTCACCTTCAGTAGGTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCATACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGTTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGTCCCGGCTGTGTATTACTGTGCGAGAGAGCCGGAACTGGTAGCACTAGTTCCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-54/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-54/partition-igh.yaml new file mode 100644 index 000000000..a7ace9329 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-54/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV2-70*01": 288, "IGHV3-7*01": 285, "IGHV4-39*01": 288}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17}}, "partitions": [{"logprob": -475.14046560761665, "n_clusters": 6, "n_procs": 1, "partition": [["3a07b6f0a9-igh"], ["453132f3ab-igh"], ["7334912e1e-igh"], ["b997fa9304-igh"], ["f094dfd68a-igh"], ["f3509e0ef3-igh"]]}, {"logprob": -442.5761164796697, "n_clusters": 5, "n_procs": 1, "partition": [["3a07b6f0a9-igh"], ["453132f3ab-igh"], ["7334912e1e-igh"], ["b997fa9304-igh", "f3509e0ef3-igh"], ["f094dfd68a-igh"]]}, {"logprob": -416.12934847327944, "n_clusters": 4, "n_procs": 1, "partition": [["3a07b6f0a9-igh", "7334912e1e-igh"], ["453132f3ab-igh"], ["b997fa9304-igh", "f3509e0ef3-igh"], ["f094dfd68a-igh"]]}, {"logprob": -392.65954039676177, "n_clusters": 3, "n_procs": 1, "partition": [["3a07b6f0a9-igh", "7334912e1e-igh", "f094dfd68a-igh"], ["453132f3ab-igh"], ["b997fa9304-igh", "f3509e0ef3-igh"]]}], "events": [{"has_shm_indels": [false, false, false], "qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["3a07b6f0a9-igh", "7334912e1e-igh", "f094dfd68a-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD1-14*01", "j_gene": "IGHJ6*02", "cdr3_length": 54, "mature_cdr3_lengths": [54, 54, 54], "mut_freqs": [0.021621621621621623, 0.032432432432432434, 0.02702702702702703], "n_mutations": [8, 12, 10], "input_seqs": ["CAGGTGCAGCTGGTGGAATCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTGCTGTGCAGCGTCTGGATTCACCTTCAGTAGGTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGAGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGTTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGTCACGGCTGTGTATTACTGTGCGAGAGAGCCGGAACCGGAACAAATAGTTGCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTCTCCTTTTCAGCGTCTGGATTCACCTTCAGTAGGTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCATACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGTTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGTCCCGGCTGTGTATTACTGTGCGAGAGAGCCGGAACTGGTAGCACTAGTTCCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGGTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGGAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGTCACGGCTGTGGATTACTGTGCGAGAGGGCCGGCACCGGAACCGCTACTTACCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGGCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGGAACCGGAACCACTAGTTGCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD1-14*01": 0.9999938922735017, "IGHD1-1*01": 4.11644715461729e-06, "IGHD6-19*01": 1.8908934650875562e-06, "IGHD2-8*01": 8.500939069912918e-08, "IGHD2-15*01": 8.558489627512363e-09, "IGHD3-9*01": 6.274499552208029e-09, "IGHD1-26*01": 5.434974464376309e-10}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 5, "d_3p_del": 0, "j_5p_del": 13, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GCCGG", "dj_insertion": "TAGTTGC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 285, "j": 336}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["b997fa9304-igh", "f3509e0ef3-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD1-14*01", "j_gene": "IGHJ6*02", "cdr3_length": 54, "mature_cdr3_lengths": [54, 54], "mut_freqs": [0.013513513513513514, 0.021621621621621623], "n_mutations": [5, 8], "input_seqs": ["CTGGTTCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGAATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATCTGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGACACAGGAACCACGAGTTCGCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "CTAGTTCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGAATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATCTGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGGGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGACACAGGAACCACGAGTTTGCTACGATATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGCCGACACAGGAACCACGAGTTCGCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD1-14*01": 0.9995170476475125, "IGHD1-1*01": 0.0003023948122658587, "IGHD3-3*01": 0.0001000888697622578, "IGHD3-16*03": 8.043259375141867e-05, "IGHD3-10*03": 3.6076719493621446e-08}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 13, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GCCGACACA", "dj_insertion": "GAGTTCG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 285, "j": 336}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["453132f3ab-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD1-14*01", "j_gene": "IGHJ6*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.016216216216216217], "n_mutations": [6], "input_seqs": ["CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACCCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGTCATGGACTGGGTCCGCCAGGCACCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAACAGGCAGCGGAACCAGAACTTTCCTACGGTATAGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAACAGGCACCGGAACCAGAACTTTCCTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD1-14*01": 0.9777748627165609, "IGHD1-1*01": 0.014925220630956105, "IGHD6-19*01": 0.0038088010013902092, "IGHD2-2*01": 0.0021935636128367383, "IGHD6-6*01": 0.0012975520382607676}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 1, "j_5p_del": 13, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "ACAGGC", "dj_insertion": "GAACTTTC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 336}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-57/igh.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-57/igh.fa new file mode 100644 index 000000000..b420644f2 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-57/igh.fa @@ -0,0 +1,24 @@ +>0eb272ee70-igh +CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGAAGTAGTAGTTCCTACTGGGGCCGGATCCGCCAGCCCCCAGGTAAGGGGGTGGAGTGGATTGGGAGTATCTATGATAGTGGTAGCACCTACTATAACCAGTCCCTCAAGAGTCGAGTCACCATATCTGTAGACGCGTCCAAGAAGCAGTTCTCCCTGAAGCTGAGCTCTGTGCCCGCCGCAGACACGGCTGCGTATTACTGTGCGAGAGAGTTGTGTATAGCAGTGCTTCTTGCTTGGATAGCCCCGGACTACTGGGGCTAGGGAACCCTGGTCACCGTCTCCTCTG +>7588f09c07-igh +CAGCTGCAGCTGCAGGAGTCGAGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCAGTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGATGAGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCCCTCCTTGGATAGCAGGGCTTCGTTCAAAGATAGCACTAGACTACTGGGACCAGGGAACCCTGGTCACCGTCTCCTCAG +>4d37fe487e-igh +CAGCTGCAGCTGCAGGAGTCGAACCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTATGGTGGCTCCATCACCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTCTTATAGTGGGAGCACATACTACAACCAGTCACTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCATGAACCAGTTCTCCCTGAAGCTGAGCTCTGTCACCGCCGCAGACACGGCTGCGTCTTACTGTGCGAGCCTGCCTAGAAGAGAAGTACCTCTTTATAAGATAGCTCAAGACTACTGGGACCAGGGAACCCTGGTCACCGTCTCCTCAG +>253ca59333-igh +CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGTTGGCTCCATCAGCAGAAGTAGTTACTACTGCGGCCCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTCGGAGTATCTATTATAGTGGGAGCACCTACTACATCCAGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCCAACCATGCATATCAGTACCTCCTACTAAACTCTCGCAAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>aa25e6c0ce-igh +CAGCTGCAGCTGCAGGAGTCGAGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACGACTGGGGCTTGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGATTCACCATATCCGTAGACCCGTCCAAGAACCAGTTCTCCCTGAAGCTGCGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCAAACATTGAATAGCAGTATCTAGTACTTCGATAGCACCGGACTACTGGGACAAGGGAACCCTGGTCACCGTCTCCTCAG +>8d79fca804-igh +CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGGTCGAGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG +>a2238f4e9a-igh +CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTTCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAAGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGTGAGCACCACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACTCCCGCAGAAACGGCGGCGTATTACTGTGCGAGAAAGCAAAGCGACACAGTACCCCCCACTGTCCTCGAACGGGACTACTGGGGCCAGGGAACCCTGGTTACCGTCTCCTCAG +>b1e56e40a1-igh +CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGACCCCAGGTAAGGGGCTGGAGTGGATTGGGACTATCTATTACATTACTGGGAGCACCTACTACGACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCACCTACTTCCATCGCTCGAGACTTCTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG +>ddcf0ca433-igh +CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGTTGGCTCCATCAGCAGAAGTAGTTACTACTGCGGCCCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTCGGAGTATCTATTATAGTGGGAGCACCTACTACATCCAGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCCAGCCTTGCATATCAGTACCTCCTACAAAACTCTCGCAAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>a3baa83300-igh +CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTAAAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCTAGCAATGTAAAACAGTACCTCCTACGTCCATCGGTCGAGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG +>b02ee7754a-igh +CAGCTGCAGCAGCAGGAGTCGGGCCCAAGGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGACTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGCTCGCGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG +>9ed10b6475-igh +CAGCTGCAGCTGCAGGAGTCGAGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTGTGGTGGCTCCATCAGCAGTAGTAGTTACGACTGGGGCTTGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGATTCACCATATCCGTAGAGCCGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCCGACACGGCTGCGTATTACTGTCCGAGTTAGCTTTGAATAGCAGTCCCTCGTACTTCGATATCACCGGACTACTGGGACAAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-57/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-57/partition-igh.yaml new file mode 100644 index 000000000..c88c3834c --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-57/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV2-70*01": 288, "IGHV3-7*01": 285, "IGHV4-39*01": 288}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17}}, "partitions": [{"logprob": -1587.4507553405374, "n_clusters": 12, "n_procs": 1, "partition": [["0eb272ee70-igh"], ["253ca59333-igh"], ["4d37fe487e-igh"], ["7588f09c07-igh"], ["8d79fca804-igh"], ["9ed10b6475-igh"], ["a2238f4e9a-igh"], ["a3baa83300-igh"], ["aa25e6c0ce-igh"], ["b02ee7754a-igh"], ["b1e56e40a1-igh"], ["ddcf0ca433-igh"]]}, {"logprob": -1547.3733731139719, "n_clusters": 11, "n_procs": 1, "partition": [["0eb272ee70-igh"], ["253ca59333-igh"], ["4d37fe487e-igh"], ["7588f09c07-igh"], ["8d79fca804-igh", "b1e56e40a1-igh"], ["9ed10b6475-igh"], ["a2238f4e9a-igh"], ["a3baa83300-igh"], ["aa25e6c0ce-igh"], ["b02ee7754a-igh"], ["ddcf0ca433-igh"]]}, {"logprob": -1502.2079780528852, "n_clusters": 10, "n_procs": 1, "partition": [["0eb272ee70-igh"], ["253ca59333-igh"], ["4d37fe487e-igh"], ["7588f09c07-igh"], ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh"], ["9ed10b6475-igh"], ["a2238f4e9a-igh"], ["aa25e6c0ce-igh"], ["b02ee7754a-igh"], ["ddcf0ca433-igh"]]}, {"logprob": -1465.8594048776556, "n_clusters": 9, "n_procs": 1, "partition": [["0eb272ee70-igh"], ["253ca59333-igh", "ddcf0ca433-igh"], ["4d37fe487e-igh"], ["7588f09c07-igh"], ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh"], ["9ed10b6475-igh"], ["a2238f4e9a-igh"], ["aa25e6c0ce-igh"], ["b02ee7754a-igh"]]}, {"logprob": -1431.7685849050504, "n_clusters": 8, "n_procs": 1, "partition": [["0eb272ee70-igh"], ["253ca59333-igh", "ddcf0ca433-igh"], ["4d37fe487e-igh"], ["7588f09c07-igh"], ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh"], ["9ed10b6475-igh", "aa25e6c0ce-igh"], ["a2238f4e9a-igh"], ["b02ee7754a-igh"]]}, {"logprob": -1381.5362461835698, "n_clusters": 7, "n_procs": 1, "partition": [["0eb272ee70-igh"], ["253ca59333-igh", "ddcf0ca433-igh"], ["4d37fe487e-igh"], ["7588f09c07-igh"], ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh", "b02ee7754a-igh"], ["9ed10b6475-igh", "aa25e6c0ce-igh"], ["a2238f4e9a-igh"]]}, {"logprob": -1353.10356989709, "n_clusters": 6, "n_procs": 1, "partition": [["0eb272ee70-igh"], ["253ca59333-igh", "ddcf0ca433-igh"], ["4d37fe487e-igh", "7588f09c07-igh"], ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh", "b02ee7754a-igh"], ["9ed10b6475-igh", "aa25e6c0ce-igh"], ["a2238f4e9a-igh"]]}, {"logprob": -1326.4148723837268, "n_clusters": 5, "n_procs": 1, "partition": [["0eb272ee70-igh", "9ed10b6475-igh", "aa25e6c0ce-igh"], ["253ca59333-igh", "ddcf0ca433-igh"], ["4d37fe487e-igh", "7588f09c07-igh"], ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh", "b02ee7754a-igh"], ["a2238f4e9a-igh"]]}, {"logprob": -1303.714842910175, "n_clusters": 4, "n_procs": 1, "partition": [["0eb272ee70-igh", "9ed10b6475-igh", "aa25e6c0ce-igh"], ["253ca59333-igh", "ddcf0ca433-igh"], ["4d37fe487e-igh", "7588f09c07-igh"], ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh", "b02ee7754a-igh", "a2238f4e9a-igh"]]}], "events": [{"has_shm_indels": [false, true, false, true, true], "qr_gap_seqs": ["", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGACCCCAGGTAAGGGGCTGGAGTGGATTGGGACTATCTATTACATTACTGGGAGCACCTACTACGACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCACCTACTTCCATCGCTCGAGACTTCTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "", "CAGCTGCAGCAGCAGGAGTCGGGCCCAAGGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGACTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGCTCGCGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTTCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAAGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGTGAGCACC.ACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACTCCCGCAGAAACGGCGGCGTATTACTGTGCGAGAAAGCAAAGCGACACAGTACCCCCCACTGTCCTCGAACGGGACTACTGGGGCCAGGGAACCCTGGTTACCGTCTCCTCAG"], "gl_gap_seqs": ["", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTA...TAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGGTCGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "CAGCTGCAGCTGCAGGAGTCGGGCCCA..GGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCAATGTATAGCAGTGGCTGGTACTGCCCTCGCTCGGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCAATGTATAGCAGTGGCTGGTACTGCCCTCGCTCGGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGACCCCAGGTAAGGGGCTGGAGTGGATTGGGACTATCTATTATACTGGGAGCACCTACTACGACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCACCTACTTCCATCGCTCGAGACTTCTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGACTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGCTCGCGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTTCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAAGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGTGAGCACCTACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACTCCCGCAGAAACGGCGGCGTATTACTGTGCGAGAAAGCAAAGCGACACAGTACCCCCCACTGTCCTCGAACGGGACTACTGGGGCCAGGGAACCCTGGTTACCGTCTCCTCAG"], "unique_ids": ["8d79fca804-igh", "b1e56e40a1-igh", "a3baa83300-igh", "b02ee7754a-igh", "a2238f4e9a-igh"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57, 57, 57, 57, 57], "mut_freqs": [0.06382978723404255, 0.08244680851063829, 0.07180851063829788, 0.07180851063829788, 0.09308510638297872], "n_mutations": [24, 31, 27, 27, 35], "input_seqs": ["CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGGTCGAGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGACCCCAGGTAAGGGGCTGGAGTGGATTGGGACTATCTATTACATTACTGGGAGCACCTACTACGACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCACCTACTTCCATCGCTCGAGACTTCTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCAGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTAAAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCTAGCAATGTAAAACAGTACCTCCTACGTCCATCGGTCGAGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCAGCAGGAGTCGGGCCCAAGGGACTGGTGATGCCTTCGGAGACCTTATCCCTCACCTGCACTGGCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAGGTAAGGGGCTGGACTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGGTCTGTGACCGCGGCAGACACGGCTGCGTATTACTGTGCGAGCGAGCAATGTAAAACAGTACCTCCTACTTCCATCGCTCGCGACTACTGGGGCCAGGGAACCCTGGTTCCCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTTCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACAGGGGCTCGATCCGCCAGCCCCCAAGTAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGTGAGCACCACTACAACCAGTCTCTCAAGAGTCGAGTCTCCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAACTGAGCTCTGTGACTCCCGCAGAAACGGCGGCGTATTACTGTGCGAGAAAGCAAAGCGACACAGTACCCCCCACTGTCCTCGAACGGGACTACTGGGGCCAGGGAACCCTGGTTACCGTCTCCTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCAATGTATAGCAGTGGCTGGTACTGCCCTCGGTCGGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], []], "leader_seqs": ["", "", "", "", ""], "c_gene_seqs": ["", "", "", "", ""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9999999999988489, "IGHD6-6*01": 6.490582037650985e-13, "IGHD2-15*01": 4.798988703384929e-13, "IGHD1-14*01": 1.7611487621819817e-14, "IGHD2-2*01": 5.606341652198298e-15, "IGHD1-1*01": 2.8421573523526843e-15, "IGHD3-9*01": 1.1076997644552306e-17}, "j_per_gene_support": {"IGHJ4*02": 0.9999711015009162, "IGHJ5*02": 2.8898499086531146e-05}, "v_3p_del": 3, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CGAGCAAT", "dj_insertion": "TGCCCTCGGTCGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false], "in_frames": [true, true, true, true, true], "stops": [false, false, true, false, false], "codon_positions": {"v": 288, "j": 342}}, {"has_shm_indels": [false, false, false], "qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["0eb272ee70-igh", "9ed10b6475-igh", "aa25e6c0ce-igh"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57, 57, 57], "mut_freqs": [0.07446808510638298, 0.06382978723404255, 0.05585106382978723], "n_mutations": [28, 24, 21], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGAAGTAGTAGTTCCTACTGGGGCCGGATCCGCCAGCCCCCAGGTAAGGGGGTGGAGTGGATTGGGAGTATCTATGATAGTGGTAGCACCTACTATAACCAGTCCCTCAAGAGTCGAGTCACCATATCTGTAGACGCGTCCAAGAAGCAGTTCTCCCTGAAGCTGAGCTCTGTGCCCGCCGCAGACACGGCTGCGTATTACTGTGCGAGAGAGTTGTGTATAGCAGTGCTTCTTGCTTGGATAGCCCCGGACTACTGGGGCTAGGGAACCCTGGTCACCGTCTCCTCTG", "CAGCTGCAGCTGCAGGAGTCGAGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTGTGGTGGCTCCATCAGCAGTAGTAGTTACGACTGGGGCTTGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGATTCACCATATCCGTAGAGCCGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCCGACACGGCTGCGTATTACTGTCCGAGTTAGCTTTGAATAGCAGTCCCTCGTACTTCGATATCACCGGACTACTGGGACAAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGAGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACGACTGGGGCTTGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCCCTCAAGAGTCGATTCACCATATCCGTAGACCCGTCCAAGAACCAGTTCTCCCTGAAGCTGCGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCAAACATTGAATAGCAGTATCTAGTACTTCGATAGCACCGGACTACTGGGACAAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCGAGCTTTGTATAGCAGTGGCTGGTACTTCGATAGCACCGGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9999997620418809, "IGHD6-6*01": 2.3418504629794938e-07, "IGHD2-2*01": 1.988273350409855e-09, "IGHD2-8*02": 1.2264705818572036e-09, "IGHD1-14*01": 3.8112594239444925e-10, "IGHD2-21*01": 1.286873575664863e-10, "IGHD2-15*01": 3.520713912076132e-11, "IGHD2-8*01": 1.236345418720092e-11, "IGHD1-26*01": 8.472485990439427e-13, "IGHD3-9*01": 1.9268662352554875e-13}, "j_per_gene_support": {"IGHJ4*02": 0.9999999924384042, "IGHJ5*02": 7.561622846458987e-09}, "v_3p_del": 3, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CGAGCTTT", "dj_insertion": "TTCGATAGCACCG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [true, true, true], "codon_positions": {"v": 288, "j": 342}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["253ca59333-igh", "ddcf0ca433-igh"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57, 57], "mut_freqs": [0.05053191489361702, 0.047872340425531915], "n_mutations": [19, 18], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGTTGGCTCCATCAGCAGAAGTAGTTACTACTGCGGCCCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTCGGAGTATCTATTATAGTGGGAGCACCTACTACATCCAGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCCAACCATGCATATCAGTACCTCCTACTAAACTCTCGCAAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGTTGGCTCCATCAGCAGAAGTAGTTACTACTGCGGCCCGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGATTCGGAGTATCTATTATAGTGGGAGCACCTACTACATCCAGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCCAGCCTTGCATATCAGTACCTCCTACAAAACTCTCGCAAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCCAGCCTTGCATAGCAGTGGCTGGTACTAAACTCTCGCAAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.8646456710709792, "IGHD2-21*01": 0.05203225393062207, "IGHD2-2*01": 0.046012716051568696, "IGHD6-6*01": 0.03384000877990313, "IGHD2-15*01": 0.0034682557233549536, "IGHD1-26*01": 1.0944435637735562e-06}, "j_per_gene_support": {"IGHJ4*02": 0.9999996327020249, "IGHJ5*02": 3.6729798603451555e-07}, "v_3p_del": 3, "d_5p_del": 4, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCAGCCTTGC", "dj_insertion": "TAAACTCTCGCAA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 288, "j": 342}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["4d37fe487e-igh", "7588f09c07-igh"], "invalid": false, "v_gene": "IGHV4-39*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57, 57], "mut_freqs": [0.07712765957446809, 0.05319148936170213], "n_mutations": [29, 20], "input_seqs": ["CAGCTGCAGCTGCAGGAGTCGAACCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTATGGTGGCTCCATCACCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTCTTATAGTGGGAGCACATACTACAACCAGTCACTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCATGAACCAGTTCTCCCTGAAGCTGAGCTCTGTCACCGCCGCAGACACGGCTGCGTCTTACTGTGCGAGCCTGCCTAGAAGAGAAGTACCTCTTTATAAGATAGCTCAAGACTACTGGGACCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGCTGCAGCTGCAGGAGTCGAGCCCAGGACTGGTGATGCCTTCGGAGACCTTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGTAAGGGGCTGGAGTGGCTTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCAGTCAGTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGATGAGCTCTGTGACCGCCGCAGACACGGCTGCGTATTACTGTGCGAGCCCTCCTTGGATAGCAGGGCTTCGTTCAAAGATAGCACTAGACTACTGGGACCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGCCCGCCTTGTATAGCAGTGGCTGGTACTAAGATAGCTCTAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV4-39*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9979158727162916, "IGHD3-16*03": 0.0011280460501943165, "IGHD6-6*01": 0.0008840090108589552, "IGHD2-2*01": 6.300312043410871e-05, "IGHD1-14*01": 8.049470041143693e-06, "IGHD2-8*01": 6.999707404741944e-07, "IGHD2-15*01": 3.191590394597858e-07, "IGHD3-10*03": 4.610745823863277e-10, "IGHD3-9*01": 4.131240482509177e-11}, "j_per_gene_support": {"IGHJ4*02": 0.99999985609379, "IGHJ5*02": 1.439061992227603e-07}, "v_3p_del": 3, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCGCCTT", "dj_insertion": "TAAGATAGCTCTA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 288, "j": 342}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-63/igh.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-63/igh.fa new file mode 100644 index 000000000..463194f31 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-63/igh.fa @@ -0,0 +1,6 @@ +>b9148494e2-igh +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG +>28f6e090f2-igh +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG +>584ba32878-igh +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-63/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-63/partition-igh.yaml new file mode 100644 index 000000000..057f0f11e --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-63/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV2-70*01": 288, "IGHV3-7*01": 285, "IGHV4-39*01": 288}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17}}, "partitions": [{"logprob": -82.41668224236362, "n_clusters": 1, "n_procs": 1, "partition": [["28f6e090f2-igh", "584ba32878-igh", "b9148494e2-igh"]]}], "events": [{"has_shm_indels": [false, false, false], "qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["28f6e090f2-igh", "584ba32878-igh", "b9148494e2-igh"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ3*02", "cdr3_length": 63, "mature_cdr3_lengths": [63, 63, 63], "mut_freqs": [0.0, 0.0, 0.0], "n_mutations": [0, 0, 0], "input_seqs": ["CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "naive_seq": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAACCGGACTGCTCTGTATAGCAGCTCGTCCCGATGGTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD6-6*01": 0.9999992846753685, "IGHD6-19*01": 7.148231158165149e-07, "IGHD1-14*01": 4.882738422431044e-10, "IGHD2-15*01": 1.2872862335923694e-11, "IGHD1-26*01": 3.67709667430218e-13}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 2, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "ACCGGACTGCTCT", "dj_insertion": "CGATGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [false, false, false], "codon_positions": {"v": 285, "j": 345}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-66/igh.fa b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-66/igh.fa new file mode 100644 index 000000000..6246d0d71 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-66/igh.fa @@ -0,0 +1,18 @@ +>4f03967793-igh +CAGGTGCAGCTGATGGTGTCTGGGGGAGGCGGGGTCCAGCCGAGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCGGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAATTATATGGTATGATGGAAGTAACAAATACTATGCAGACTCCGTGAAGGGCTGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGGTGGAGGGGATCTCTGGACTGGTCTTTATGGGAACAACTGGTTCGACCCCTGGGGACAGGGAACCCTGGTCACCGTCTCCTCAG +>c2cc9da0c3-igh +CAGGTGCAGCTGGTGGGGTCTGGGGGAGGCGTGGTCCAGCCTGGTAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTGACCTTATGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGAGTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAATTGAACAGCTTGAGAGCCGAGGAGACGGCTGTGAATTACTGTCCGAGAGAGGGTGGATTCGAATTATGGATTTGATAGTATGGTACCAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAT +>c0fcfe005f-igh +CAGGTGCAGCTGGCGGAGTCTGGGGGAGGCGTGGTCCACCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCATCTGGATTCACCGTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTGCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCCGGGTGAGATTTTGGGTTTGGTTACTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>7c67587674-igh +CGGGTGCAGCTGATGGAGTCTGGGGGAGGCGTGGTACAGCCTGGGAGGTCCCTGAGACTCTCCTATGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCGGCCAGGCTCCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATGCGCCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGATGCGTTTTTTGGAATGGTCCGTCAAGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>6cf028b770-igh +CAGGCGCAGCGGATGGAGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCAGGATTCACCTTCAGTAGCTATGGCATGCACCGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATCTTGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGACAAGCCTGAGAGCCGAGGACACGGATGTGAATTACTGTGCGAGAGATACTGGCGGCGATTTTTCGAATGGCCTTTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>d1ee7f9ce6-igh +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCACCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCATCTGGATTCACCGTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGGTGAGATTTTGGGTTTGCTTACTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>6577576bb8-igh +CAGGTGTAGCTGATGGTGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTGACTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGCCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTATTATATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGAGGCGATTTGTGGAATGGTATTTTCGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>cdae60eacc-igh +CGGGTGCAGCTGATGGAGTCTGGGGGAGGCGTGGTACAGCCTGGGAGGTCCCTGAGACTCTCCTATGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCGGCCAGGCTCCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATGCGCCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGATGCGTTTTTTGGAATGGTCCGTCAAGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>665985d2d1-igh +CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCACCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCATCTGGATTCACCGTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGGTTAGATTTTGGGTTTGGTTAGTGTGCGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-66/partition-igh.yaml b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-66/partition-igh.yaml new file mode 100644 index 000000000..68526ceed --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/groups/cdr3-66/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-69*04": "CAGGTCCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGTCCTCGGTGAAGGTCTCCTGCAAGGCTTCTGGAGGCACCTTCAGCAGCTATGCTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGAAGGATCATCCCTATCCTTGGTATAGCAAACTACGCACAGAAGTTCCAGGGCAGAGTCACGATTACCGCGGACAAATCCACGAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-70*01": "CAGGTCACCTTGAGGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGTGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACTCATTGATTGGGATGATGATAAATACTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-33*01": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*01": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV4-39*01": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCCGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGACA"}, "d": {"IGHD1-1*01": "GGTACAACTGGAACGAC", "IGHD1-14*01": "GGTATAACCGGAACCAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*03": "GTATTATGATTACATTTGGGGGAGTTATCGTTATACC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD3-9*01": "GTATTACGATATTTTGACTGGTTATTATAAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC", "IGHD7-27*01": "CTAACTGGGGA"}, "j": {"IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-69*04": 285, "IGHV1-2*02": 285, "IGHV3-33*01": 285, "IGHV2-70*01": 288, "IGHV3-7*01": 285, "IGHV4-39*01": 288}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17}}, "partitions": [{"logprob": -910.761027913789, "n_clusters": 8, "n_procs": 1, "partition": [["4f03967793-igh"], ["6577576bb8-igh"], ["665985d2d1-igh"], ["6cf028b770-igh"], ["7c67587674-igh", "cdae60eacc-igh"], ["c0fcfe005f-igh"], ["c2cc9da0c3-igh"], ["d1ee7f9ce6-igh"]]}, {"logprob": -877.5811319649233, "n_clusters": 7, "n_procs": 1, "partition": [["4f03967793-igh"], ["6577576bb8-igh"], ["665985d2d1-igh"], ["6cf028b770-igh"], ["7c67587674-igh", "cdae60eacc-igh"], ["c0fcfe005f-igh", "d1ee7f9ce6-igh"], ["c2cc9da0c3-igh"]]}, {"logprob": -853.430345163235, "n_clusters": 6, "n_procs": 1, "partition": [["4f03967793-igh", "c2cc9da0c3-igh"], ["6577576bb8-igh"], ["665985d2d1-igh"], ["6cf028b770-igh"], ["7c67587674-igh", "cdae60eacc-igh"], ["c0fcfe005f-igh", "d1ee7f9ce6-igh"]]}, {"logprob": -831.3736173396267, "n_clusters": 5, "n_procs": 1, "partition": [["4f03967793-igh", "c2cc9da0c3-igh", "6cf028b770-igh"], ["6577576bb8-igh"], ["665985d2d1-igh"], ["7c67587674-igh", "cdae60eacc-igh"], ["c0fcfe005f-igh", "d1ee7f9ce6-igh"]]}, {"logprob": -802.3667074260454, "n_clusters": 4, "n_procs": 1, "partition": [["4f03967793-igh", "c2cc9da0c3-igh", "6cf028b770-igh", "6577576bb8-igh"], ["665985d2d1-igh"], ["7c67587674-igh", "cdae60eacc-igh"], ["c0fcfe005f-igh", "d1ee7f9ce6-igh"]]}, {"logprob": -789.6279824528732, "n_clusters": 3, "n_procs": 1, "partition": [["4f03967793-igh", "c2cc9da0c3-igh", "6cf028b770-igh", "6577576bb8-igh", "c0fcfe005f-igh", "d1ee7f9ce6-igh"], ["665985d2d1-igh"], ["7c67587674-igh", "cdae60eacc-igh"]]}, {"logprob": -768.3267451376103, "n_clusters": 2, "n_procs": 1, "partition": [["4f03967793-igh", "c2cc9da0c3-igh", "6cf028b770-igh", "6577576bb8-igh", "c0fcfe005f-igh", "d1ee7f9ce6-igh", "665985d2d1-igh"], ["7c67587674-igh", "cdae60eacc-igh"]]}], "events": [{"has_shm_indels": [false, false, false, true, false, false, false], "qr_gap_seqs": ["", "", "", "CAGGTGTAGCTGATGGTGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTGACTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGCCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTATTATATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGAGGCGATTTGTGGAATGGTATTTTCGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["", "", "", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACT..CTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGCCGGGGGCGATTTTTGGAGTGGTTATTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["", "", "", "CAGGTGTAGCTGATGGTGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGCCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTATTATATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGAGGCGATTTGTGGAATGGTATTTTCGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["4f03967793-igh", "c2cc9da0c3-igh", "6cf028b770-igh", "6577576bb8-igh", "c0fcfe005f-igh", "d1ee7f9ce6-igh", "665985d2d1-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ5*02", "cdr3_length": 66, "mature_cdr3_lengths": [66, 66, 66, 66, 66, 66, 66], "mut_freqs": [0.060209424083769635, 0.06282722513089005, 0.06282722513089005, 0.049738219895287955, 0.034031413612565446, 0.028795811518324606, 0.034031413612565446], "n_mutations": [23, 24, 24, 19, 13, 11, 13], "input_seqs": ["CAGGTGCAGCTGATGGTGTCTGGGGGAGGCGGGGTCCAGCCGAGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCGGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAATTATATGGTATGATGGAAGTAACAAATACTATGCAGACTCCGTGAAGGGCTGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGGTGGAGGGGATCTCTGGACTGGTCTTTATGGGAACAACTGGTTCGACCCCTGGGGACAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGGGTCTGGGGGAGGCGTGGTCCAGCCTGGTAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTGACCTTATGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGAGTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAATTGAACAGCTTGAGAGCCGAGGAGACGGCTGTGAATTACTGTCCGAGAGAGGGTGGATTCGAATTATGGATTTGATAGTATGGTACCAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAT", "CAGGCGCAGCGGATGGAGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCAGGATTCACCTTCAGTAGCTATGGCATGCACCGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATCTTGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGACAAGCCTGAGAGCCGAGGACACGGATGTGAATTACTGTGCGAGAGATACTGGCGGCGATTTTTCGAATGGCCTTTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGTAGCTGATGGTGTCTGGGGGAGGCGTGGTCCAGCCTAGGAGGTCCCTGAGACTGACTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGCCATGCACTGGGTCCGCCAGGCACCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTATTATATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACCCGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGAGGCGATTTGTGGAATGGTATTTTCGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGCGGAGTCTGGGGGAGGCGTGGTCCACCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCATCTGGATTCACCGTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTGCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCCGGGTGAGATTTTGGGTTTGGTTACTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCACCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCATCTGGATTCACCGTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGGTGAGATTTTGGGTTTGCTTACTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCACCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCATCTGGATTCACCGTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGGTTAGATTTTGGGTTTGGTTAGTGTGCGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGCTGGGGGCGATTTTTGGAGTGGTTATTATGGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9999999999983515, "IGHD7-27*01": 8.308376385077691e-13, "IGHD3-16*03": 6.948266534158579e-13, "IGHD6-19*01": 1.3360536198414565e-13, "IGHD2-8*02": 6.433253481148827e-15, "IGHD2-15*01": 4.265508477870675e-15, "IGHD2-2*01": 2.4756584348163524e-15, "IGHD2-8*01": 2.2742933639680054e-15, "IGHD3-9*01": 1.8099647951750524e-15, "IGHD2-21*01": 1.7532292880581524e-15, "IGHD3-10*03": 4.237639904204738e-16}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 6, "d_3p_del": 3, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGCTGGGGG", "dj_insertion": "GGGA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [true, true, false, true, true, true, true], "codon_positions": {"v": 285, "j": 348}}, {"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["7c67587674-igh", "cdae60eacc-igh"], "invalid": false, "v_gene": "IGHV3-33*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ5*02", "cdr3_length": 66, "mature_cdr3_lengths": [66, 66], "mut_freqs": [0.028795811518324606, 0.028795811518324606], "n_mutations": [11, 11], "input_seqs": ["CGGGTGCAGCTGATGGAGTCTGGGGGAGGCGTGGTACAGCCTGGGAGGTCCCTGAGACTCTCCTATGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCGGCCAGGCTCCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATGCGCCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGATGCGTTTTTTGGAATGGTCCGTCAAGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CGGGTGCAGCTGATGGAGTCTGGGGGAGGCGTGGTACAGCCTGGGAGGTCCCTGAGACTCTCCTATGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCGGCCAGGCTCCCGCCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATGCGCCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGAATTACTGTGCGAGAGAGGCTGGATGCGTTTTTTGGAATGGTCCGTCAAGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCGTGGTCCAGCCTGGGAGGTCCCTGAGACTCTCCTGTGCAGCGTCTGGATTCACCTTCAGTAGCTATGGCATGCACTGGGTCCGCCAGGCTCCAGGCAAGGGGCTGGAGTGGGTGGCAGTTATATGGTATGATGGAAGTAATAAATACTATGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGAGGCTGGATGCGTTTTTTGGAGTGGTCCGTCAAGGAACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-33*01": 1.0}, "d_per_gene_support": {"IGHD3-3*01": 0.9997233702522996, "IGHD6-19*01": 0.00023668470338459078, "IGHD2-8*01": 2.8778508903320612e-05, "IGHD3-9*01": 7.920884587635916e-06, "IGHD2-15*01": 3.2456508168783846e-06}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 9, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GGCTGGATGCGT", "dj_insertion": "CCGTCAAGGA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 285, "j": 348}}]} \ No newline at end of file diff --git a/test/paired/ref-results/disjoint-group-new-simu/manifest.yaml b/test/paired/ref-results/disjoint-group-new-simu/manifest.yaml new file mode 100644 index 000000000..1f5afddf0 --- /dev/null +++ b/test/paired/ref-results/disjoint-group-new-simu/manifest.yaml @@ -0,0 +1,92 @@ +assembly: + merged_output_path: assembled/ + status: merged + validation: + gene_lists_consistent: null + sequence_count_preserved: true + uids_unique: true +grouping-info: + failed_sequences: 0 + loci: + - igh + - igk + - igl + method: cdr3-length + parameter_dir: test/paired/ref-results/test/parameters/simu + total_grouped_sequences: 113 + total_input_sequences: 113 +groups: +- cdr3_length: 33 + fasta_path: groups/cdr3-33/igh.fa + group_id: 0 + locus: igh + partition_path: groups/cdr3-33/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 39 + fasta_path: groups/cdr3-39/igh.fa + group_id: 1 + locus: igh + partition_path: groups/cdr3-39/partition-igh.yaml + sequence_count: 13 +- cdr3_length: 48 + fasta_path: groups/cdr3-48/igh.fa + group_id: 2 + locus: igh + partition_path: groups/cdr3-48/partition-igh.yaml + sequence_count: 12 +- cdr3_length: 54 + fasta_path: groups/cdr3-54/igh.fa + group_id: 3 + locus: igh + partition_path: groups/cdr3-54/partition-igh.yaml + sequence_count: 6 +- cdr3_length: 57 + fasta_path: groups/cdr3-57/igh.fa + group_id: 4 + locus: igh + partition_path: groups/cdr3-57/partition-igh.yaml + sequence_count: 12 +- cdr3_length: 63 + fasta_path: groups/cdr3-63/igh.fa + group_id: 5 + locus: igh + partition_path: groups/cdr3-63/partition-igh.yaml + sequence_count: 3 +- cdr3_length: 66 + fasta_path: groups/cdr3-66/igh.fa + group_id: 6 + locus: igh + partition_path: groups/cdr3-66/partition-igh.yaml + sequence_count: 9 +- cdr3_length: 30 + fasta_path: groups/cdr3-30/igk.fa + group_id: 0 + locus: igk + partition_path: groups/cdr3-30/partition-igk.yaml + sequence_count: 3 +- cdr3_length: 33 + fasta_path: groups/cdr3-33/igk.fa + group_id: 1 + locus: igk + partition_path: groups/cdr3-33/partition-igk.yaml + sequence_count: 24 +- cdr3_length: 36 + fasta_path: groups/cdr3-36/igk.fa + group_id: 2 + locus: igk + partition_path: groups/cdr3-36/partition-igk.yaml + sequence_count: 9 +- cdr3_length: 33 + fasta_path: groups/cdr3-33/igl.fa + group_id: 0 + locus: igl + partition_path: groups/cdr3-33/partition-igl.yaml + sequence_count: 3 +- cdr3_length: 39 + fasta_path: groups/cdr3-39/igl.fa + group_id: 1 + locus: igl + partition_path: groups/cdr3-39/partition-igl.yaml + sequence_count: 18 +version-info: + partis-yaml: 0.2 diff --git a/test/ref-results/disjoint-group-new-data/assembled/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/assembled/partition-igh.yaml new file mode 100644 index 000000000..a958413e3 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/assembled/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": 0.0, "n_clusters": 40, "n_procs": 1, "partition": [["crap-2"], ["-7103133300489454258"], ["-8009227471980910973", "-897112141984688730", "8251691699452868973", "944860330169026868"], ["06-B-M_3768642"], ["2895171606369249876", "indel-1"], ["02-C-M_2027377"], ["02-C-M_2188593"], ["11.d0"], ["8851231630392144693"], ["-2126437327330379358"], ["1441.d0"], ["1591.d28"], ["61.d0"], ["04-A-M_4022824"], ["1081.d0"], ["1201.d7"], ["211.d0"], ["02-C-M_3856399"], ["04-A-M_3275309"], ["-7829267785575297546"], ["1491.d0"], ["591.d0"], ["8520939472988791669", "indel-2"], ["1.d0"], ["1221.d7"], ["1951.d0"], ["3213257196707376594"], ["631.d0"], ["-2746509048448212099"], ["-4847562276697408608"], ["-9140119851721454527"], ["02-C-M_3281471"], ["06-B-M_2962542"], ["901.d0"], ["02-C-M_1115713"], ["04-A-M_2148159"], ["06-B-M_0345150"], ["02-C-M_0360936"], ["-991144955841202245", "6785281000938532760"], ["6731449281791440313"]]}], "events": [{"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["crap-2"], "invalid": false, "v_gene": "IGHV3-11*04", "d_gene": "IGHD5-5*01", "j_gene": "IGHJ3*02", "cdr3_length": 32, "mature_cdr3_lengths": [32], "mut_freqs": [0.4661016949152542], "n_mutations": [55], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGCTGTGTATTACTGTGAGCCGAGGACACGGCTGTGTATTACTGTGAGCCGAGGACACGGCTGTGTATTACTGTGAGCCGAGGACACGGCTGTGTATTACTGTGA"], "has_shm_indels": [false], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGAGCTATGGTTACTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-11*04": 0.9973905731149263, "IGHV3-66*02": 0.002131104610144013, "IGHV3-69-1*02": 0.0004783222749039372}, "d_per_gene_support": {"IGHD5-5*01": 0.9267065035832495, "IGHD2-2*01": 0.02900774625532391, "IGHD2-8*01": 0.020910844637413335, "IGHD2-8*02": 0.014999965582069796, "IGHD2-15*01": 0.008374939941915809}, "j_per_gene_support": {"IGHJ3*02": 0.9999935516704427, "IGHJ4*02": 6.4483295296532145e-06}, "v_3p_del": 7, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [true], "in_frames": [false], "stops": [true], "codon_positions": {"v": 285, "j": 314}}, {"qr_gap_seqs": ["", "", "", ""], "gl_gap_seqs": ["", "", "", ""], "indel_reversed_seqs": ["", "", "", ""], "unique_ids": ["-8009227471980910973", "-897112141984688730", "8251691699452868973", "944860330169026868"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33, 33], "mut_freqs": [0.09248554913294797, 0.10115606936416185, 0.1069364161849711, 0.1531791907514451], "n_mutations": [32, 35, 37, 53], "input_seqs": ["GAGGTGCAACTGGTGGAGTTTGGTGGAGCCTTGGTCCTGCGTAGGGGGTCCCTGCGACTCTCCTGTGCAGCCTCTCGATTCACCGTTGGTAGCAACTACATCAGCTGGGTCCGCCAGGCTCCACGGAAGGGGCTGGATTGGCTCTCAGTCATTTATAGAGGTGGTAACACATACTACGCAGATTCCTTGGAGAGCCGATTCAGCATCTCTAGAGACAATTCGAAGAACACGCTGTATCTTCAAATGATCAGCCTGAGAGCTAAGGACACAGCTGTGTATTACTGTGCGAGACCTATAACAGCAGCCGTCTAATGGGGCCAGGGATCCCTGGTCACCGTCTCCTCAG", "GAGGCGCAACTGGTGGAGTTTGGTGGAGCCTTGGTGCTGCGTAGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTCGATTCACCGTTGGTAGCAACTACATGAGCTGGGTCCGCCAGACTCCACGGAAGGGGCTGGATTGGCTCTCAGTTATTTATGGCGGTGGTAACACATACTACGCAGATTCCTTGAAGGGCCGATTCACCATCTCTACAGACAATTCCAAGAACACGTTGTATCTTCAAATGATCAGCCTGAGACTTAACGACACGGCTGTGTATTACTGTGCGAGACCTAAAACAGCAGCCGTCAAATGGGGCCTGGGATCCCTGGTCACCGTCTCCTCAG", "GAGGTGCAACTGGTGGAGTTTGGTGGAGCCTTGGTTCTGCGTAGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTCGATTCACCGTAGGTAGCAACTAGATGAGCTAGGTCCGCCAGGCTCCACGGAAGGGGCTTGATTGCCTCTCAGTTATTTATAGCGGCGGCAACACATACTACGCAGATTCCTTGAAGGGCCGATTCACCATCTCTAGAGACAATTCTAAGAGCACGCTGTATCTTCAAATGATCAGCCAGAGAACTAAGGACACGGCTGTGTATTACTGTGCGAGACCGATAACAGCACCCGGCTAATGGGGCCAGGGATCCCTGGTCACCGTCTCCTCAG", "GAGGTGTAACTGATGAAGTCTGGAGGAGGCTTGGTCCTGCGTGGGGGGTCCCTGGGACTCTCCTGTACAGCCCCTAGATTCACCGCCAATAACAACTACATGACCTTGGTCCCCCAGGCTCCATGGAAGAGGCTCGTGTGGGTTTCAGTGATTTGTAGCGGTGGTAGCACTTACTGCTCAGATTCCGTCCAGGGCTGATTCCCCATCTCCAAAGATAATTCCAAGAACATGCTGTATCTTCCAATGTACAGCCTGAGAGCTGAGGATATAGCTGTGTACTACTGTACGAGACCGTTATCAGCGACCGGTTATTGGGGCCGGGGAACCGAGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGACCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], []], "leader_seqs": ["", "", "", ""], "c_gene_seqs": ["", "", "", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9984552000683292, "IGHD6-6*01": 0.00147973095578162, "IGHD6-19*01": 6.258893864923332e-05, "IGHD2-15*01": 1.096869884106676e-06, "IGHD1-20*01": 5.780450706763637e-07, "IGHD3-22*01": 4.964554952858319e-07, "IGHD2-2*01": 1.1164618881357458e-07, "IGHD3-3*01": 1.0062078458930902e-07, "IGHD3-16*02": 7.541391767889976e-08, "IGHD4-4*01": 2.0985901236870694e-08}, "j_per_gene_support": {"IGHJ4*02": 0.9999955713972434, "IGHJ5*02": 4.428602756050557e-06}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false], "in_frames": [true, true, true, true], "stops": [true, false, true, true], "codon_positions": {"v": 282, "j": 312}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["-7103133300489454258"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD4-4*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.08959537572254335], "n_mutations": [31], "input_seqs": ["GAGGTGCAACTGGTGGAGTTTGGTGGAGCCTTGGTCCTGCGTAGGGGGTGCCTGAGACTCTCCTCTGCAGCCTCTCGATTCGCCGTTCGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCACGGAACGGGCTGGATTCGCTCTCAGTTATTTATAGCGCTGGTAACACATACTACGCAGATTCCTTGAAGGGCCGATTCATCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTTAAATGATCAGCCTGAGACCTAAGGACACGGCTGTGCATTACTGTGCGAGACTGACAACAGCGGCGGCCCCATGGGGCCAGGGATCCCTGGTCACCGTCTCCTCAG"], 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+GAGCCGAGGACACGGCTGTGTATTACTGTGAGCCGAGGACACGGCTGTGTATTACTGTGAGCCGAGGACACGGCTGTGTATTACTGTGAGCCGAGGACACGGCTGTGTATTACTGTGA diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-32/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-32/partition-igh.yaml new file mode 100644 index 000000000..afd8994b6 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-32/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -476.96745454016354, "n_clusters": 1, "n_procs": 1, "partition": [["crap-2"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["crap-2"], "invalid": false, "v_gene": "IGHV3-11*04", "d_gene": "IGHD5-5*01", "j_gene": "IGHJ3*02", "cdr3_length": 32, "mature_cdr3_lengths": [32], "mut_freqs": [0.4661016949152542], "n_mutations": [55], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGCTGTGTATTACTGTGAGCCGAGGACACGGCTGTGTATTACTGTGAGCCGAGGACACGGCTGTGTATTACTGTGAGCCGAGGACACGGCTGTGTATTACTGTGA"], "naive_seq": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGAGCTATGGTTACTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-11*04": 0.9973905731149263, "IGHV3-66*02": 0.002131104610144013, "IGHV3-69-1*02": 0.0004783222749039372}, "d_per_gene_support": {"IGHD5-5*01": 0.9267065035832495, "IGHD2-2*01": 0.02900774625532391, "IGHD2-8*01": 0.020910844637413335, "IGHD2-8*02": 0.014999965582069796, "IGHD2-15*01": 0.008374939941915809}, "j_per_gene_support": {"IGHJ3*02": 0.9999935516704427, "IGHJ4*02": 6.4483295296532145e-06}, "v_3p_del": 7, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [true], "in_frames": [false], "stops": [true], "codon_positions": {"v": 285, "j": 314}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-33/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-33/igh.fa new file mode 100644 index 000000000..cbdba7d24 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-33/igh.fa @@ -0,0 +1,10 @@ +>944860330169026868 +GAGGTGTAACTGATGAAGTCTGGAGGAGGCTTGGTCCTGCGTGGGGGGTCCCTGGGACTCTCCTGTACAGCCCCTAGATTCACCGCCAATAACAACTACATGACCTTGGTCCCCCAGGCTCCATGGAAGAGGCTCGTGTGGGTTTCAGTGATTTGTAGCGGTGGTAGCACTTACTGCTCAGATTCCGTCCAGGGCTGATTCCCCATCTCCAAAGATAATTCCAAGAACATGCTGTATCTTCCAATGTACAGCCTGAGAGCTGAGGATATAGCTGTGTACTACTGTACGAGACCGTTATCAGCGACCGGTTATTGGGGCCGGGGAACCGAGGTCACCGTCTCCTCAG +>-8009227471980910973 +GAGGTGCAACTGGTGGAGTTTGGTGGAGCCTTGGTCCTGCGTAGGGGGTCCCTGCGACTCTCCTGTGCAGCCTCTCGATTCACCGTTGGTAGCAACTACATCAGCTGGGTCCGCCAGGCTCCACGGAAGGGGCTGGATTGGCTCTCAGTCATTTATAGAGGTGGTAACACATACTACGCAGATTCCTTGGAGAGCCGATTCAGCATCTCTAGAGACAATTCGAAGAACACGCTGTATCTTCAAATGATCAGCCTGAGAGCTAAGGACACAGCTGTGTATTACTGTGCGAGACCTATAACAGCAGCCGTCTAATGGGGCCAGGGATCCCTGGTCACCGTCTCCTCAG +>-897112141984688730 +GAGGCGCAACTGGTGGAGTTTGGTGGAGCCTTGGTGCTGCGTAGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTCGATTCACCGTTGGTAGCAACTACATGAGCTGGGTCCGCCAGACTCCACGGAAGGGGCTGGATTGGCTCTCAGTTATTTATGGCGGTGGTAACACATACTACGCAGATTCCTTGAAGGGCCGATTCACCATCTCTACAGACAATTCCAAGAACACGTTGTATCTTCAAATGATCAGCCTGAGACTTAACGACACGGCTGTGTATTACTGTGCGAGACCTAAAACAGCAGCCGTCAAATGGGGCCTGGGATCCCTGGTCACCGTCTCCTCAG +>-7103133300489454258 +GAGGTGCAACTGGTGGAGTTTGGTGGAGCCTTGGTCCTGCGTAGGGGGTGCCTGAGACTCTCCTCTGCAGCCTCTCGATTCGCCGTTCGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCACGGAACGGGCTGGATTCGCTCTCAGTTATTTATAGCGCTGGTAACACATACTACGCAGATTCCTTGAAGGGCCGATTCATCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTTAAATGATCAGCCTGAGACCTAAGGACACGGCTGTGCATTACTGTGCGAGACTGACAACAGCGGCGGCCCCATGGGGCCAGGGATCCCTGGTCACCGTCTCCTCAG +>8251691699452868973 +GAGGTGCAACTGGTGGAGTTTGGTGGAGCCTTGGTTCTGCGTAGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTCGATTCACCGTAGGTAGCAACTAGATGAGCTAGGTCCGCCAGGCTCCACGGAAGGGGCTTGATTGCCTCTCAGTTATTTATAGCGGCGGCAACACATACTACGCAGATTCCTTGAAGGGCCGATTCACCATCTCTAGAGACAATTCTAAGAGCACGCTGTATCTTCAAATGATCAGCCAGAGAACTAAGGACACGGCTGTGTATTACTGTGCGAGACCGATAACAGCACCCGGCTAATGGGGCCAGGGATCCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-33/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-33/partition-igh.yaml new file mode 100644 index 000000000..e493659b4 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-33/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -774.0966142201788, "n_clusters": 4, "n_procs": 1, "partition": [["-7103133300489454258"], ["-8009227471980910973", "-897112141984688730"], ["8251691699452868973"], ["944860330169026868"]]}, {"logprob": -753.1246808705083, "n_clusters": 3, "n_procs": 1, "partition": [["-7103133300489454258"], ["-8009227471980910973", "-897112141984688730", "8251691699452868973"], ["944860330169026868"]]}, {"logprob": -738.084331997356, "n_clusters": 2, "n_procs": 1, "partition": [["-7103133300489454258"], ["-8009227471980910973", "-897112141984688730", "8251691699452868973", "944860330169026868"]]}], "events": [{"has_shm_indels": [false, false, false, false], "qr_gap_seqs": ["", "", "", ""], "gl_gap_seqs": ["", "", "", ""], "indel_reversed_seqs": ["", "", "", ""], "unique_ids": ["-8009227471980910973", "-897112141984688730", "8251691699452868973", "944860330169026868"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33, 33], "mut_freqs": [0.09248554913294797, 0.10115606936416185, 0.1069364161849711, 0.1531791907514451], "n_mutations": [32, 35, 37, 53], "input_seqs": ["GAGGTGCAACTGGTGGAGTTTGGTGGAGCCTTGGTCCTGCGTAGGGGGTCCCTGCGACTCTCCTGTGCAGCCTCTCGATTCACCGTTGGTAGCAACTACATCAGCTGGGTCCGCCAGGCTCCACGGAAGGGGCTGGATTGGCTCTCAGTCATTTATAGAGGTGGTAACACATACTACGCAGATTCCTTGGAGAGCCGATTCAGCATCTCTAGAGACAATTCGAAGAACACGCTGTATCTTCAAATGATCAGCCTGAGAGCTAAGGACACAGCTGTGTATTACTGTGCGAGACCTATAACAGCAGCCGTCTAATGGGGCCAGGGATCCCTGGTCACCGTCTCCTCAG", "GAGGCGCAACTGGTGGAGTTTGGTGGAGCCTTGGTGCTGCGTAGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTCGATTCACCGTTGGTAGCAACTACATGAGCTGGGTCCGCCAGACTCCACGGAAGGGGCTGGATTGGCTCTCAGTTATTTATGGCGGTGGTAACACATACTACGCAGATTCCTTGAAGGGCCGATTCACCATCTCTACAGACAATTCCAAGAACACGTTGTATCTTCAAATGATCAGCCTGAGACTTAACGACACGGCTGTGTATTACTGTGCGAGACCTAAAACAGCAGCCGTCAAATGGGGCCTGGGATCCCTGGTCACCGTCTCCTCAG", "GAGGTGCAACTGGTGGAGTTTGGTGGAGCCTTGGTTCTGCGTAGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTCGATTCACCGTAGGTAGCAACTAGATGAGCTAGGTCCGCCAGGCTCCACGGAAGGGGCTTGATTGCCTCTCAGTTATTTATAGCGGCGGCAACACATACTACGCAGATTCCTTGAAGGGCCGATTCACCATCTCTAGAGACAATTCTAAGAGCACGCTGTATCTTCAAATGATCAGCCAGAGAACTAAGGACACGGCTGTGTATTACTGTGCGAGACCGATAACAGCACCCGGCTAATGGGGCCAGGGATCCCTGGTCACCGTCTCCTCAG", "GAGGTGTAACTGATGAAGTCTGGAGGAGGCTTGGTCCTGCGTGGGGGGTCCCTGGGACTCTCCTGTACAGCCCCTAGATTCACCGCCAATAACAACTACATGACCTTGGTCCCCCAGGCTCCATGGAAGAGGCTCGTGTGGGTTTCAGTGATTTGTAGCGGTGGTAGCACTTACTGCTCAGATTCCGTCCAGGGCTGATTCCCCATCTCCAAAGATAATTCCAAGAACATGCTGTATCTTCCAATGTACAGCCTGAGAGCTGAGGATATAGCTGTGTACTACTGTACGAGACCGTTATCAGCGACCGGTTATTGGGGCCGGGGAACCGAGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGACCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], []], "leader_seqs": ["", "", "", ""], "c_gene_seqs": ["", "", "", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9984552000683292, "IGHD6-6*01": 0.00147973095578162, "IGHD6-19*01": 6.258893864923332e-05, "IGHD2-15*01": 1.096869884106676e-06, "IGHD1-20*01": 5.780450706763637e-07, "IGHD3-22*01": 4.964554952858319e-07, "IGHD2-2*01": 1.1164618881357458e-07, "IGHD3-3*01": 1.0062078458930902e-07, "IGHD3-16*02": 7.541391767889976e-08, "IGHD4-4*01": 2.0985901236870694e-08}, "j_per_gene_support": {"IGHJ4*02": 0.9999955713972434, "IGHJ5*02": 4.428602756050557e-06}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false], "in_frames": [true, true, true, true], "stops": [true, false, true, true], "codon_positions": {"v": 282, "j": 312}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["-7103133300489454258"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD4-4*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mature_cdr3_lengths": [33], "mut_freqs": [0.08959537572254335], "n_mutations": [31], "input_seqs": ["GAGGTGCAACTGGTGGAGTTTGGTGGAGCCTTGGTCCTGCGTAGGGGGTGCCTGAGACTCTCCTCTGCAGCCTCTCGATTCGCCGTTCGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCACGGAACGGGCTGGATTCGCTCTCAGTTATTTATAGCGCTGGTAACACATACTACGCAGATTCCTTGAAGGGCCGATTCATCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTTAAATGATCAGCCTGAGACCTAAGGACACGGCTGTGCATTACTGTGCGAGACTGACAACAGCGGCGGCCCCATGGGGCCAGGGATCCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGACTGACTACAGCGGCGGCCCCATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD4-4*01": 0.8186117414506648, "IGHD6-13*01": 0.1600864380685583, "IGHD4-17*01": 0.02059814261245092, "IGHD6-19*01": 0.00045994052436653293, "IGHD2-2*01": 0.00024373734394876514}, "j_per_gene_support": {"IGHJ4*02": 0.9646588667690075, "IGHJ5*02": 0.03534113323098482}, "v_3p_del": 2, "d_5p_del": 0, "d_3p_del": 7, "j_5p_del": 14, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "C", "dj_insertion": "CGGCGGCCCCA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "codon_positions": {"v": 282, "j": 312}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-39/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-39/igh.fa new file mode 100644 index 000000000..b70850cea --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-39/igh.fa @@ -0,0 +1,6 @@ +>2895171606369249876 +GAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGATCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGGTTCACCTTCAGTAGCCACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCTGCGGTAGCACATACTACGCAGACTCCATGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGGTTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAAATACGATAACTGCCTGATACGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>indel-1 +GAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGATCCAGCCTGGGGGGTCCCTGAGACTGTGCAGCCTCTGGGTTCACCTTCAGTAGCCACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCTGCGGTAGCACATACTACGCAGACTCCATGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGGTTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAAATACGATAACTGCCTGATACGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>06-B-M_3768642 +CACCATGACCACAGACACATCCACGAGCACAGCCTTCATGACACTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTACGAGAGACAGAAACTATTACGGTCTGGACGTCTGGGGCCAAGGG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igh.yaml new file mode 100644 index 000000000..6a3d6ecad --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-39/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -534.7226629961655, "n_clusters": 2, "n_procs": 1, "partition": [["06-B-M_3768642"], ["2895171606369249876", "indel-1"]]}], "events": [{"has_shm_indels": [false, true], "qr_gap_seqs": ["", "NNNGAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGATCCAGCCTGGGGGGTCCCTGAGA.....CTGTGCAGCCTCTGGGTTCACCTTCAGTAGCCACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCTGCGGTAGCACATACTACGCAGACTCCATGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGGTTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAAATACGATAACTGCCTGATACGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["", "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAATACGATAACTGCCTGATACGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "NNNGAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGATCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGGTTCACCTTCAGTAGCCACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCTGCGGTAGCACATACTACGCAGACTCCATGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGGTTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAAATACGATAACTGCCTGATACGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["2895171606369249876", "indel-1"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD1-20*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39], "mut_freqs": [0.03409090909090909, 0.03409090909090909], "n_mutations": [12, 12], "input_seqs": ["NNNGAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGATCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGGTTCACCTTCAGTAGCCACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCTGCGGTAGCACATACTACGCAGACTCCATGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGGTTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAAATACGATAACTGCCTGATACGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "NNNGAGGTGCAGCTGGTGGAGTCTGGAGGAGGCTTGATCCAGCCTGGGGGGTCCCTGAGACTGTGCAGCCTCTGGGTTCACCTTCAGTAGCCACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCTGCGGTAGCACATACTACGCAGACTCCATGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGGTTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAAATACGATAACTGCCTGATACGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAATACGATAACTGCCTGATACGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD1-20*01": 0.9789148851037538, "IGHD3-3*01": 0.017660450387402837, "IGHD4-4*01": 0.0028755377438577268, "IGHD4-17*01": 0.00048222315162204705, "IGHD6-19*01": 6.690361336316689e-05}, "j_per_gene_support": {"IGHJ4*02": 0.999999451936426, "IGHJ5*02": 5.480635727474212e-07}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 7, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AATACG", "dj_insertion": "CCTGATAC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, false], "stops": [true, true], "codon_positions": {"v": 285, "j": 321}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["06-B-M_3768642"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD4-4*01", "j_gene": "IGHJ6*02", "cdr3_length": 39, "mature_cdr3_lengths": [39], "mut_freqs": [0.05384615384615385], "n_mutations": [7], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCACCATGACCACAGACACATCCACGAGCACAGCCTTCATGACACTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTACGAGAGACAGAAACTATTACGGTCTGGACGTCTGGGGCCAAGGGNNNNNNNNNNNNNNNNNNNNNN"], "naive_seq": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACAGTAACTATTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-18*01": 1.0}, "d_per_gene_support": {"IGHD4-4*01": 0.4552854843072209, "IGHD5-5*01": 0.2672398741766407, "IGHD6-13*01": 0.14369725063530903, "IGHD6-19*01": 0.07723986117447594, "IGHD1-20*01": 0.0565375297063892}, "j_per_gene_support": {"IGHJ6*02": 0.9999993556428224, "IGHJ6*03": 6.443571754279027e-07}, "v_3p_del": 0, "d_5p_del": 7, "d_3p_del": 1, "j_5p_del": 14, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "C", "dj_insertion": "T", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 321}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-42/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-42/igh.fa new file mode 100644 index 000000000..128ddc119 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-42/igh.fa @@ -0,0 +1,8 @@ +>02-C-M_2188593 +CATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGTACTCTACAGTATTTATTGCTATGGACGTCTGGGGCCAAGGG +>8851231630392144693 +CAGGTGCAGCTGGTGCAGTCTGGGTCTGAGGTGAAGACGCCTGGGGCCTCAGTGAAGCTCTCCTGCAAGGCTTCTGGATACTTCTTCACCGACTACTATATGCAGTGGGTGCGACAGGCCCTTGGACAAGAGCTTGGGTGGATGGGACGGATCAACCCTAACAGTGGTGGCATAAACTATGCACAGAAGTTTCAAGGCAGAGTCACCATGACGAGGGACATGTCCATCAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCACGTATTACTGTGCGTACGGTGTCTGGCCTTTGTTCTACTTTGACTACTGGGGCCAGGGTACCCTGGTCACCGTCTCCTCAG +>11.d0 +GAGCCGAGGACACGGCCGTATATTACTGTGCCCGATCGGCCCTAGGTAGTAGAGGACTCTTCCACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>02-C-M_2027377 +CATCTTTAGAGACAGTTCCAAGAACACGCTGCATCTGCAAATGAACGGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAGGAATTATGCCAGCTGCTCGGGTTCGACCCCTGGGGCCAGGGA diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-42/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-42/partition-igh.yaml new file mode 100644 index 000000000..a9fadc746 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-42/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -1330.2111710465583, "n_clusters": 4, "n_procs": 1, "partition": [["02-C-M_2027377"], ["02-C-M_2188593"], ["11.d0"], ["8851231630392144693"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["02-C-M_2027377"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-3*01", "j_gene": "IGHJ5*02", "cdr3_length": 42, "mature_cdr3_lengths": [42], "mut_freqs": [0.05384615384615385], "n_mutations": [7], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATCTTTAGAGACAGTTCCAAGAACACGCTGCATCTGCAAATGAACGGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAGGAATTATGCCAGCTGCTCGGGTTCGACCCCTGGGGCCAGGGANNNNNNNNNNNNNNNNNNNNNN"], "naive_seq": "NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTATACCAGCTGCTCGGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-23*01": 0.999999993764618, "IGHV3-66*02": 6.235394386067729e-09}, "d_per_gene_support": {"IGHD3-3*01": 0.28344865414511766, "IGHD6-13*01": 0.26898806017173776, "IGHD2-2*01": 0.2382479629959329, "IGHD6-6*01": 0.16108190988128662, "IGHD2-15*01": 0.04823341280595504}, "j_per_gene_support": {"IGHJ5*02": 0.9999852806958394, "IGHJ4*02": 1.4719304132144406e-05}, "v_3p_del": 0, "d_5p_del": 23, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "AGCTGCTCG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 327}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["02-C-M_2188593"], "invalid": false, "v_gene": "IGHV2-70D*04", "d_gene": "IGHD4-4*01", "j_gene": "IGHJ6*02", "cdr3_length": 42, "mature_cdr3_lengths": [42], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGTACTCTACAGTATTTATTGCTATGGACGTCTGGGGCCAAGGGNNNNNNNNNNNNNNNNNNNNNN"], "naive_seq": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGTACTCTACAGTATTTATTGCTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-70D*04": 0.999999997234454, "IGHV2-5*02": 2.7655287163494958e-09}, "d_per_gene_support": {"IGHD4-4*01": 0.9937219026110942, "IGHD3-22*01": 0.0048777370422689835, "IGHD4-17*01": 0.0009560370527900542, "IGHD3-3*01": 0.00033252820063820143, "IGHD5-5*01": 0.00011179509317525946}, "j_per_gene_support": {"IGHJ6*02": 0.999994616524471, "IGHJ6*03": 5.383475527744507e-06}, "v_3p_del": 4, "d_5p_del": 3, "d_3p_del": 5, "j_5p_del": 19, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TACT", "dj_insertion": "TTTATTGC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 327}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["11.d0"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ4*02", "cdr3_length": 42, "mature_cdr3_lengths": [42], "mut_freqs": [0.010101010101010102], "n_mutations": [1], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGCCGTATATTACTGTGCCCGATCGGCCCTAGGTAGTAGAGGACTCTTCCACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCCCGATCGGCCCTAGGTAGTAGTGGACTCTTCCACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-23*01": 0.9907014193687583, "IGHV3-7*05": 0.008661762264956718, "IGHV3-11*04": 0.0006368183662918217}, "d_per_gene_support": {"IGHD3-22*01": 0.8473995904866993, "IGHD6-6*01": 0.10542779962979994, "IGHD2-2*01": 0.035385543284444064, "IGHD2-15*01": 0.011777269438163915, "IGHD6-19*01": 9.797160844091028e-06}, "j_per_gene_support": {"IGHJ4*02": 0.9903382522944593, "IGHJ5*02": 0.009661747705528603}, "v_3p_del": 6, "d_5p_del": 12, "d_3p_del": 10, "j_5p_del": 12, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGATCGGCCCTAGG", "dj_insertion": "ACTCTTCC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 327}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["8851231630392144693"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD4-17*01", "j_gene": "IGHJ4*02", "cdr3_length": 42, "mature_cdr3_lengths": [42], "mut_freqs": [0.061452513966480445], "n_mutations": [22], "input_seqs": ["NNNCAGGTGCAGCTGGTGCAGTCTGGGTCTGAGGTGAAGACGCCTGGGGCCTCAGTGAAGCTCTCCTGCAAGGCTTCTGGATACTTCTTCACCGACTACTATATGCAGTGGGTGCGACAGGCCCTTGGACAAGAGCTTGGGTGGATGGGACGGATCAACCCTAACAGTGGTGGCATAAACTATGCACAGAAGTTTCAAGGCAGAGTCACCATGACGAGGGACATGTCCATCAGCACAGCCTACATGGAGCTGAGCAGCCTGAGATCTGAGGACACGGCCACGTATTACTGTGCGTACGGTGTCTGGCCTTTGTTCTACTTTGACTACTGGGGCCAGGGTACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGTACGGTGACTGGCCTTTGTTCTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD4-17*01": 0.9555148850595343, "IGHD2-8*01": 0.033962580392732596, "IGHD6-19*01": 0.004553587308857536, "IGHD2-21*02": 0.004065291059756315, "IGHD2-8*02": 0.0019036561790874112}, "j_per_gene_support": {"IGHJ4*02": 0.9999999994386712, "IGHJ1*01": 5.613194176219733e-10}, "v_3p_del": 5, "d_5p_del": 4, "d_3p_del": 2, "j_5p_del": 1, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GGCCTTTGTT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 327}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-45/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-45/igh.fa new file mode 100644 index 000000000..915e94881 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-45/igh.fa @@ -0,0 +1,8 @@ +>-2126437327330379358 +CCTCATCTACTAACTCCCTGCCTTAGGTTGGTGTTGTATGTGTGGAAAAATCATCTGGTTTTCTGCCTGTCTCGCGGTCGTTAGACCATTCGTTCTTGTTGCTGCAACTGCTTGCTTTTGCCCCTAGGCACGCGGGCAGGTAGGCTTCAAGACCTTTATTCCAATCCTAGCTCGGACTTTATCTCTTTCTACTCCCTAGTGCATGTCACGTCAGGTGTGTCGTTTCCGGGATAACCCCGACTGATTCTCCTCTCTGTTTGATCTTTTGACTAGGGGCTCTGTACCTGTGCGATAGATAGTTACCGGCCCGCATGGTGCTTCCGCATGTGGGGACGGGGGGCCCTGGTCGCTGTCTCCCCAG +>1591.d28 +GAGCCGAGGACACGGCCGTCTATTACTGTGCGAAAGATACGTCTCACAGCAGCTGGGTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAA +>61.d0 +GAGCCGAGGACACGGCTATTTATTACTGTGCGAGACACGTCCGCCAACTGGTGGCGTTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>1441.d0 +GAGCCGAGGACACGGGTGTTTATTACTGTGCGACATCATCATATTGTAGTGTCAGCAGTTGCTTTGACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-45/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-45/partition-igh.yaml new file mode 100644 index 000000000..c0eeb3e08 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-45/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -1768.6241220345457, "n_clusters": 4, "n_procs": 1, "partition": [["-2126437327330379358"], ["1441.d0"], ["1591.d28"], ["61.d0"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["-2126437327330379358"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD5-5*01", "j_gene": "IGHJ1*01", "cdr3_length": 35, "mature_cdr3_lengths": [35], "mut_freqs": [0.6581196581196581], "n_mutations": [231], "input_seqs": ["NNNCCTCATCTACTAACTCCCTGCCTTAGGTTGGTGTTGTATGTGTGGAAAAATCATCTGGTTTTCTGCCTGTCTCGCGGTCGTTAGACCATTCGTTCTTGTTGCTGCAACTGCTTGCTTTTGCCCCTAGGCACGCGGGCAGGTAGGCTTCAAGACCTTTATTCCAATCCTAGCTCGGACTTTATCTCTTTCTACTCCCTAGTGCATGTCACGTCAGGTGTGTCGTTTCCGGGATAACCCCGACTGATTCTCCTCTCTGTTTGATCTTTTGACTAGGGGCTCTGTACCTGTGCGATAGATAGTTACCGGCCCGCATGGTGCTTCCGCATGTGGGGACGGGGGGCCCTGGTCGCTGTCTCCCCAG"], "naive_seq": "NNNCAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACAGCTATGGTTACTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAGNNNNNNNNNN", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-18*01": 0.5163813849676189, "IGHV4-61*01": 0.4836186150323697, "IGHV1-2*02": 7.283810157119455e-19}, "d_per_gene_support": {"IGHD5-5*01": 0.5521869286345624, 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["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGGTGTTTATTACTGTGCGACATCATCATATTGTAGTGTCAGCAGTTGCTTTGACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGATCATCATATTGTAGTGGTGGTAGCTGCTTTGACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-69-1*02": 0.9769253648280162, "IGHV3-11*04": 0.021162701245180677, "IGHV3-23*01": 0.0019119339268251845}, "d_per_gene_support": {"IGHD2-15*01": 0.976596943452372, "IGHD2-2*01": 0.015563260209546658, "IGHD2-21*02": 0.004899092685947549, "IGHD2-21*01": 0.0020420557516402722, "IGHD2-8*02": 0.0008986479004164887}, "j_per_gene_support": {"IGHJ4*02": 0.9979747826904724, "IGHJ5*02": 0.0020252173095259354}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 5, "j_5p_del": 12, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCATC", "dj_insertion": "TTG", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 330}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["1591.d28"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 45, "mature_cdr3_lengths": [45], "mut_freqs": [0.0196078431372549], "n_mutations": [2], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGCCGTCTATTACTGTGCGAAAGATACGTCTCACAGCAGCTGGGTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAA"], "naive_seq": "NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGATACGTCTCACAGCAGCTGGGTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-23*01": 0.9988350949075319, "IGHV3-7*05": 0.0011200515318851765, "IGHV3-11*04": 4.485356057372157e-05}, "d_per_gene_support": {"IGHD6-13*01": 0.9787657706128724, "IGHD6-6*01": 0.021218561905753195, "IGHD2-2*01": 1.2629705759909897e-05, "IGHD6-19*01": 2.9340028150304258e-06, "IGHD5-5*01": 1.037728025061587e-07}, "j_per_gene_support": {"IGHJ4*02": 0.9999999602692932, "IGHJ5*02": 3.973072418077116e-08}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 3, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TACGTCTCA", "dj_insertion": "GT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 330}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["61.d0"], "invalid": false, "v_gene": "IGHV3-69-1*02", "d_gene": "IGHD2-8*02", "j_gene": "IGHJ4*02", "cdr3_length": 45, "mature_cdr3_lengths": [45], "mut_freqs": [0.00980392156862745], "n_mutations": [1], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGCTATTTATTACTGTGCGAGACACGTCCGCCAACTGGTGGCGTTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGACACGTCCGCCAACTGGTGGCGTTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-69-1*02": 0.9970442782365074, "IGHV3-11*04": 0.0029516731540826235, "IGHV3-7*05": 4.048609380954723e-06}, "d_per_gene_support": {"IGHD2-8*02": 0.722733662430988, "IGHD6-13*01": 0.10299359233043917, "IGHD1-20*01": 0.10097488029026433, "IGHD2-21*01": 0.04390985471683797, "IGHD2-15*01": 0.02938801023150408}, "j_per_gene_support": {"IGHJ4*02": 0.9999999878158407, "IGHJ5*02": 1.2184185309928652e-08}, "v_3p_del": 2, "d_5p_del": 10, "d_3p_del": 13, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CACGTCCGCCA", "dj_insertion": "CGTT", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 330}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-48/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-48/igh.fa new file mode 100644 index 000000000..c86449973 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-48/igh.fa @@ -0,0 +1,8 @@ +>04-A-M_4022824 +AGTCGACAACTCCATCAACACCGCCTACCTGCAGTGGAGCAGTGTGGAGGCCTCGGACACCGCCATGTATTTTTGCGCGCGGCTGGGGTTTAGTGGTGGCTGGTACGGGTTTGACTCCTGGGGCCAGGGA +>211.d0 +GAGCCGAGGACACGGCTATTTATTACTGTGTGAGAGACCGAGAAGGCGTACGAGCTACCGTCTTTGACTCCTGGGGCCCGGGAACCCTGGTCACCGTCTCCTCAG +>1201.d7 +GAGACGAGGACACGGCCGTATATTACTGTGCGAAAGATCCCAACGGTGACTATGTAGGTGGTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTGCAG +>1081.d0 +TGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGCGTAATCCCCGGGTATAGCAGCAGCTGGTACCGCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-48/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-48/partition-igh.yaml new file mode 100644 index 000000000..5e346daeb --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-48/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -1696.9194460479494, "n_clusters": 4, "n_procs": 1, "partition": [["04-A-M_4022824"], ["1081.d0"], ["1201.d7"], ["211.d0"]]}], "events": [{"has_shm_indels": [false], 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"NNNGAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTGGGGTATAGCAGTGGCTGGTACGGCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV5-51*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9809139073336935, "IGHD6-13*01": 0.018508196640421, "IGHD1-26*01": 0.0005066943564606042, "IGHD2-15*01": 7.012153666402712e-05, "IGHD2-21*02": 1.0801327762891704e-06}, "j_per_gene_support": {"IGHJ4*02": 0.8846278441176595, "IGHJ5*02": 0.11537215588235622}, "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TG", "dj_insertion": "GG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": 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"NNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGCGTAATCCCCGGGTATAGCAGCAGCTGGTACCGCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-4*09": 0.996301319941747, "IGHV4-39*09": 0.0035431555978410172, "IGHV4-34*01": 0.00015552446040300973}, "d_per_gene_support": {"IGHD6-13*01": 0.9987162286872794, "IGHD6-6*01": 0.001262403802126826, "IGHD6-19*01": 1.7316641263725905e-05, "IGHD1-26*01": 3.227819919756776e-06, "IGHD1-20*01": 8.230494145814412e-07}, "j_per_gene_support": {"IGHJ4*02": 0.9994156512154472, "IGHJ5*02": 0.0005843487845546107}, "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 7, "j_5p_del": 10, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CGTAATCCCC", "dj_insertion": "CTGGTACCG", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["1201.d7"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD4-17*01", "j_gene": "IGHJ3*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.02857142857142857], "n_mutations": [3], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGACGAGGACACGGCCGTATATTACTGTGCGAAAGATCCCAACGGTGACTATGTAGGTGGTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTGCAG"], "naive_seq": "NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGATCCCAACGGTGACTATGTAGGTGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-23*01": 0.9999781901433435, "IGHV3-7*05": 2.053656072877854e-05, "IGHV3-11*04": 1.2732959156071192e-06}, "d_per_gene_support": {"IGHD4-17*01": 0.9986331689149165, "IGHD3-10*01": 0.0004991989890502951, "IGHD3-10*03": 0.0003926009854551842, "IGHD3-22*01": 0.0003029675766153544, "IGHD2-21*02": 0.00017206353392850457}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 0, "d_5p_del": 5, "d_3p_del": 1, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCCCA", "dj_insertion": "TGTAGG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["211.d0"], "invalid": false, "v_gene": "IGHV3-69-1*02", "d_gene": "IGHD1-26*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.0380952380952381], "n_mutations": [4], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGCTATTTATTACTGTGTGAGAGACCGAGAAGGCGTACGAGCTACCGTCTTTGACTCCTGGGGCCCGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGACCGAGAAGGCGTACGAGCTACCGTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-69-1*02": 0.992594031676738, "IGHV3-11*04": 0.007217970002751312, "IGHV3-66*02": 0.00018799832050373842}, "d_per_gene_support": {"IGHD1-26*01": 0.9734602770544428, "IGHD2-2*01": 0.017908850280252624, "IGHD2-15*01": 0.00398288336163128, "IGHD2-8*01": 0.0030675924009899505, "IGHD3-16*02": 0.0015803969026817527}, "j_per_gene_support": {"IGHJ4*02": 0.9999410246487528, "IGHJ5*02": 5.8975351231389164e-05}, "v_3p_del": 0, "d_5p_del": 10, "d_3p_del": 3, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGAGAAGGCGTAC", "dj_insertion": "CGT", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 333}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-51/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-51/igh.fa new file mode 100644 index 000000000..449a12624 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-51/igh.fa @@ -0,0 +1,4 @@ +>04-A-M_3275309 +CACCACCCCCGGGGCCACCCCCTACATGAAACGGGGGACCCTGAGGTCTGACGACACGGCCATATATTACTGTGCGAGAGATAGAGGGCAGCACCTGACCCCTCTTTACTTTGACTTCTGGGGCCAGGGA +>02-C-M_3856399 +AGAGACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTCTATTACTGTGCGAGAGACGACCGTCTGTATAGTAGCAGTACTACACTTGACTACTGGGGCCAGGGA diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-51/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-51/partition-igh.yaml new file mode 100644 index 000000000..3cfa1ddae --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-51/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -831.2652287451067, "n_clusters": 2, "n_procs": 1, "partition": [["02-C-M_3856399"], ["04-A-M_3275309"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["02-C-M_3856399"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mature_cdr3_lengths": [51], "mut_freqs": [0.023076923076923078], "n_mutations": [3], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGAGACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTCTATTACTGTGCGAGAGACGACCGTCTGTATAGTAGCAGTACTACACTTGACTACTGGGGCCAGGGANNNNNNNNNNNNNNNNNNNNNN"], "naive_seq": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACGACCGTCTGTATAGCAGCAGTACTACACTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-18*01": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9729313222116946, "IGHD6-6*01": 0.02519162243400524, "IGHD2-2*01": 0.0009410617650773, "IGHD1-26*01": 0.0009117918917211582, "IGHD6-19*01": 2.420169749521475e-05}, "j_per_gene_support": {"IGHJ4*02": 0.999999369726282, "IGHJ5*02": 6.302737234374495e-07}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 7, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CGACCGTCT", "dj_insertion": "TACTACAC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 333}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["04-A-M_3275309"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mature_cdr3_lengths": [51], "mut_freqs": [0.2], "n_mutations": [26], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCACCACCCCCGGGGCCACCCCCTACATGAAACGGGGGACCCTGAGGTCTGACGACACGGCCATATATTACTGTGCGAGAGATAGAGGGCAGCACCTGACCCCTCTTTACTTTGACTTCTGGGGCCAGGGANNNNNNNNNNNNNNNNNNNNNN"], "naive_seq": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGATAGATAGCAGCAGCTGGTACCTCTTTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-18*01": 0.9996229380773844, "IGHV1-2*02": 0.00037706192261781807}, "d_per_gene_support": {"IGHD6-13*01": 0.973650690124261, "IGHD6-6*01": 0.020749115203004813, "IGHD2-15*01": 0.0051085755343245635, "IGHD1-26*01": 0.00047250242723724636, "IGHD2-21*02": 1.9116711189882564e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999980564122796, "IGHJ5*02": 1.943587737526326e-06}, "v_3p_del": 0, "d_5p_del": 4, "d_3p_del": 0, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TAG", "dj_insertion": "CTCTT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 333}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-54/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-54/igh.fa new file mode 100644 index 000000000..81dc3ab09 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-54/igh.fa @@ -0,0 +1,10 @@ +>591.d0 +TGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGGTGTGACTATGGTTCGGGGAGGCTCACACCTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>1491.d0 +GAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATCCCTGGTATAGCAGTTCGTCCGCTGCTCCTTTTGACATCTGGGGCCAAGGGACAAAGGTCACCGTCTCTTCAG +>8520939472988791669 +CAAGTGCGACTGATACAGTCTGGGTCTCAACTGCAGAAGCCTGGGGCCTCACTGACTCTATCCTGTTTAGCTTCCGGATATGCCTTCGTCCGATATTGTGTTGATTGGGTTCGACAGTGACCTGGGTCGTTATCTGACTGGATGGGCTGGCTCAATCCTAGCGGTGGTGGCGTAATCTAGACAAGGAATTTCCCGGGCAGATTCACTGTGTTACGTGACAAGATCCTCAGTACACTATATGTCGATGTGGGTAGTCTGATATCTGACGACACGGCCGTTTATTATTGTGTGAGGCAAGAATTTTGTAGTTACTGTGTTCTCTACACCCACCTGTACTGGGGACAGGGGATTCTGGTCTTCGTCTCTTCAG +>indel-2 +CAAGTGCGACTGATACAGTCTGGGTCTCAACTGCAGAAGCCTGGGGCCTCACTGACTCTATCCTGTTTAGCTTCCGGATATGCCTTCGTCCGATATTGTGGGGGGTTGATTGGGTTCGACAGTGACCTGGGTCGTTATCTGACTGGATGGGCTGGCTCAATCCTAGCGGTGGTGGCGTAATCTAGACAAGGAATTTCCCGGGCAGATTCACTGTGTTACGTGACAAGATCCTCAGTACACTATATGTCGATGTGGGTAGTCTGATATCTGACGACACGGCCGTTTATTATTGTGTGAGGCAAGAATTTTGTAGTTACTGTGTTCTCTACACCCACCTGTACTGGGGACAGGGGATTCTGGTCTTCGTCTCTTCAG +>-7829267785575297546 +GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGATCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGACCGGTTCACCATCTCCAGAGACAATTCCAAAAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGGGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTCTGGGGGAGTTATCGTTATACTTCTATGCCTACTGGGGCCAGGGTACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-54/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-54/partition-igh.yaml new file mode 100644 index 000000000..fcaab9076 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-54/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -1480.8269060529008, "n_clusters": 4, "n_procs": 1, "partition": [["-7829267785575297546"], ["1491.d0"], ["591.d0"], ["8520939472988791669", "indel-2"]]}], "events": [{"has_shm_indels": [false, true], "qr_gap_seqs": ["", "NNNCAAGTGCGACTGATACAGTCTGGGTCTCAACTGCAGAAGCCTGGGGCCTCACTGACTCTATCCTGTTTAGCTTCCGGATATGCCTTCGTCCGATATTGTGGGGGGTTGATTGGGTTCGACAGTGACCTGGGTCGTTATCTGACTGGATGGGCTGGCTCAATCCTAGCGGTGGTGGCGTAATCTAGACAAGGAATTTCCCGGGCAGATTCACTGTGTTACGTGACAAGATCCTCAGTACACTATATGTCGATGTGGGTAGTCTGATATCTGACGACACGGCCGTTTATTATTGTGTGAGGCAAGAATTTTGTAGTTACTGTGTTCTCTACACCCACCTGTACTGGGGACAGGGGATTCTGGTCTTCGTCTCTTCAG"], "gl_gap_seqs": ["", "NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTAT.....ATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGGCAAGGATATTGTACTAATGGTGTATGCTATACCCTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["", "NNNCAAGTGCGACTGATACAGTCTGGGTCTCAACTGCAGAAGCCTGGGGCCTCACTGACTCTATCCTGTTTAGCTTCCGGATATGCCTTCGTCCGATATTGTGTTGATTGGGTTCGACAGTGACCTGGGTCGTTATCTGACTGGATGGGCTGGCTCAATCCTAGCGGTGGTGGCGTAATCTAGACAAGGAATTTCCCGGGCAGATTCACTGTGTTACGTGACAAGATCCTCAGTACACTATATGTCGATGTGGGTAGTCTGATATCTGACGACACGGCCGTTTATTATTGTGTGAGGCAAGAATTTTGTAGTTACTGTGTTCTCTACACCCACCTGTACTGGGGACAGGGGATTCTGGTCTTCGTCTCTTCAG"], "unique_ids": ["8520939472988791669", "indel-2"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD2-8*01", "j_gene": "IGHJ1*01", "cdr3_length": 54, "mature_cdr3_lengths": [54, 54], "mut_freqs": [0.2972972972972973, 0.2972972972972973], "n_mutations": [110, 110], "input_seqs": ["NNNCAAGTGCGACTGATACAGTCTGGGTCTCAACTGCAGAAGCCTGGGGCCTCACTGACTCTATCCTGTTTAGCTTCCGGATATGCCTTCGTCCGATATTGTGTTGATTGGGTTCGACAGTGACCTGGGTCGTTATCTGACTGGATGGGCTGGCTCAATCCTAGCGGTGGTGGCGTAATCTAGACAAGGAATTTCCCGGGCAGATTCACTGTGTTACGTGACAAGATCCTCAGTACACTATATGTCGATGTGGGTAGTCTGATATCTGACGACACGGCCGTTTATTATTGTGTGAGGCAAGAATTTTGTAGTTACTGTGTTCTCTACACCCACCTGTACTGGGGACAGGGGATTCTGGTCTTCGTCTCTTCAG", "NNNCAAGTGCGACTGATACAGTCTGGGTCTCAACTGCAGAAGCCTGGGGCCTCACTGACTCTATCCTGTTTAGCTTCCGGATATGCCTTCGTCCGATATTGTGGGGGGTTGATTGGGTTCGACAGTGACCTGGGTCGTTATCTGACTGGATGGGCTGGCTCAATCCTAGCGGTGGTGGCGTAATCTAGACAAGGAATTTCCCGGGCAGATTCACTGTGTTACGTGACAAGATCCTCAGTACACTATATGTCGATGTGGGTAGTCTGATATCTGACGACACGGCCGTTTATTATTGTGTGAGGCAAGAATTTTGTAGTTACTGTGTTCTCTACACCCACCTGTACTGGGGACAGGGGATTCTGGTCTTCGTCTCTTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGGCAAGGATATTGTACTAATGGTGTATGCTATACCCTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD2-8*01": 0.9999975491904726, "IGHD2-15*01": 9.664614253245865e-07, "IGHD2-2*01": 8.84015314103383e-07, "IGHD2-8*02": 5.685790684663248e-07, "IGHD3-3*01": 3.175373595003274e-08}, "j_per_gene_support": {"IGHJ1*01": 0.9991111004268257, "IGHJ4*02": 0.0008888995731840877}, "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 10, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GCA", "dj_insertion": "C", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, false], "stops": [true, true], "codon_positions": {"v": 288, "j": 339}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["-7829267785575297546"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-16*02", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.021621621621621623], "n_mutations": [8], "input_seqs": ["NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGATCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGACCGGTTCACCATCTCCAGAGACAATTCCAAAAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGGGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTCTGGGGGAGTTATCGTTATACTTCTATGCCTACTGGGGCCAGGGTACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCTCTATGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-23*01": 1.0}, "d_per_gene_support": {"IGHD3-16*02": 1.0}, "j_per_gene_support": {"IGHJ4*02": 0.9997122100923342, "IGHJ1*01": 0.0002877899076594801}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "TCTA", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 339}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["1491.d0"], "invalid": false, "v_gene": "IGHV3-11*04", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ3*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.04504504504504504], "n_mutations": [5], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATCCCTGGTATAGCAGTTCGTCCGCTGCTCCTTTTGACATCTGGGGCCAAGGGACAAAGGTCACCGTCTCTTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGATCCCTGGTATAGCAGCTCGTCCGCTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-11*04": 0.9412994274256146, "IGHV3-66*02": 0.03550729932991027, "IGHV3-69-1*02": 0.023193273244514333}, "d_per_gene_support": {"IGHD6-6*01": 0.9991698757876802, "IGHD6-13*01": 0.0007598507930014845, "IGHD6-19*01": 6.967594170858263e-05, "IGHD1-26*01": 5.055466747319573e-07, "IGHD3-22*01": 9.193100664954096e-08}, "j_per_gene_support": {"IGHJ3*02": 0.9999999304941436, "IGHJ6*02": 6.950583927874148e-08}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCCCTG", "dj_insertion": "GC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 339}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["591.d0"], "invalid": false, "v_gene": "IGHV4-39*09", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mature_cdr3_lengths": [54], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGGTGTGACTATGGTTCGGGGAGGCTCACACCTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGGTGTGACTATGGTTCGGGGAGGCTCACACCTCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-39*09": 0.99237715012463, "IGHV4-61*01": 0.0075349426936028065, "IGHV4-34*01": 8.790718180945295e-05}, "d_per_gene_support": {"IGHD3-10*01": 0.9986687648503347, "IGHD3-10*03": 0.0013274677193331294, "IGHD4-17*01": 3.656620776939466e-06, "IGHD3-16*02": 8.951898403544072e-08, "IGHD5-5*01": 2.1290537281447098e-08}, "j_per_gene_support": {"IGHJ4*02": 0.99999999683223, "IGHJ5*02": 3.1677888909645564e-09}, "v_3p_del": 1, "d_5p_del": 5, "d_3p_del": 10, "j_5p_del": 4, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTGTG", "dj_insertion": "GCTCACACCT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 339}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-57/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-57/igh.fa new file mode 100644 index 000000000..445b2df68 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-57/igh.fa @@ -0,0 +1,10 @@ +>1951.d0 +TGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGCCCCAGGCCGATTACTATGGTTCGGGGAGTCACCCCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>3213257196707376594 +GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGACCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCTTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACCGGTGGTAGCTGCTACTCCAAGCTTTTTCTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG +>1.d0 +GAGCTGAGGACACGGCCGTCTATTACTGTGCAAAAGATAGAGCCTTTGATTGGGTGGTCCAGGGAGTCACGATCGACCTCTGGGGCCAGGGGACCCTGGTCACCGTCTCCTCAG +>631.d0 +GAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGATATCCTAGAGGACTCGAGTATAGCAGCCCTACCCTCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>1221.d7 +GAGCCGAGGACACGGCTGTGTATTACTGTGCGACCGGCGGTATTGCAACAGCTGGTAACTGGCGGTCGGGTGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-57/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-57/partition-igh.yaml new file mode 100644 index 000000000..a7d5e75ba --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-57/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -1778.1982050298705, "n_clusters": 5, "n_procs": 1, "partition": [["1.d0"], ["1221.d7"], ["1951.d0"], ["3213257196707376594"], ["631.d0"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["1.d0"], "invalid": false, "v_gene": "IGHV3-9*02", "d_gene": "IGHD3-10*03", "j_gene": "IGHJ5*02", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.043859649122807015], "n_mutations": [5], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCTGAGGACACGGCCGTCTATTACTGTGCAAAAGATAGAGCCTTTGATTGGGTGGTCCAGGGAGTCACGATCGACCTCTGGGGCCAGGGGACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNGAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATAGAGCCTTTGATTGGGTGGTTCAGGGAGTCACGATCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-9*02": 0.9956338154397333, "IGHV3-23*01": 0.0043555876358285835, "IGHV3-7*05": 1.0596924460522084e-05}, "d_per_gene_support": {"IGHD3-10*03": 0.8503754915828058, "IGHD3-10*01": 0.1487715647076497, "IGHD2-21*01": 0.0005249464648746843, "IGHD2-15*01": 0.0002918833644697871, "IGHD6-19*01": 3.6113880243689426e-05}, "j_per_gene_support": {"IGHJ5*02": 0.9991621857706113, "IGHJ1*01": 0.0008378142293658693}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 9, "j_5p_del": 9, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GAGCCTTTGATTGGG", "dj_insertion": "CACGA", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 342}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["1221.d7"], "invalid": false, "v_gene": "IGHV3-11*04", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.02631578947368421], "n_mutations": [3], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGCTGTGTATTACTGTGCGACCGGCGGTATTGCAACAGCTGGTAACTGGCGGTCGGGTGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGACCGGCGGTATAGCAGCAGCTGGTACCTGGCGGTCGGGTGGTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-11*04": 0.9801258331384809, "IGHV3-66*02": 0.01108091173608002, "IGHV3-69-1*02": 0.008793255125444913}, "d_per_gene_support": {"IGHD6-13*01": 0.9999969793853584, "IGHD1-20*01": 1.9731939757656105e-06, "IGHD6-19*01": 9.303360047511785e-07, "IGHD2-15*01": 7.745729996501573e-08, "IGHD2-2*01": 3.9627361091482696e-08}, "j_per_gene_support": {"IGHJ4*02": 0.9999998179772712, "IGHJ5*02": 1.8202274556933176e-07}, "v_3p_del": 4, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCGGC", "dj_insertion": "CTGGCGGTCGGGTGG", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 342}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["1951.d0"], "invalid": false, "v_gene": "IGHV4-34*01", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGCCCCAGGCCGATTACTATGGTTCGGGGAGTCACCCCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNCAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGCCCCAGGCCGATTACTATGGTTCGGGGAGTCACCCCTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-34*01": 0.9995681163954452, "IGHV4-39*09": 0.0003913297602224157, "IGHV4-4*09": 4.055384434288993e-05}, "d_per_gene_support": {"IGHD3-10*01": 0.9993659756612553, "IGHD3-10*03": 0.0006340243321885927, "IGHD3-16*02": 6.548269986170027e-12}, "j_per_gene_support": {"IGHJ4*02": 0.9999996867916743, "IGHJ5*02": 3.1320831858388133e-07}, "v_3p_del": 1, "d_5p_del": 2, "d_3p_del": 9, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCCAGGCCG", "dj_insertion": "CACCCC", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 342}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["3213257196707376594"], "invalid": false, "v_gene": "IGHV5-51*01", "d_gene": "IGHD2-15*01", "j_gene": "IGHJ2*01", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.005361930294906166], "n_mutations": [2], "input_seqs": ["NNNGAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGACCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCTTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACCGGTGGTAGCTGCTACTCCAAGCTTTTTCTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG"], "naive_seq": "NNNGAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACCGGTGGTAGCTGCTACTCCAAGCTTTTTCTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV5-51*01": 1.0}, "d_per_gene_support": {"IGHD2-15*01": 0.9999999870094812, "IGHD2-21*02": 9.785158744397982e-09, "IGHD1-26*01": 3.061018868039533e-09, "IGHD2-21*01": 1.3944400222614586e-10, "IGHD2-8*02": 4.892581620545596e-12}, "j_per_gene_support": {"IGHJ2*01": 1.0}, "v_3p_del": 1, "d_5p_del": 13, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "C", "dj_insertion": "AAGCTTTTT", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 342}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["631.d0"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-6*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGATATCCTAGAGGACTCGAGTATAGCAGCCCTACCCTCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGATATCCTAGAGGACTCGAGTATAGCAGCCCTACCCTCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-66*02": 0.9976890386400032, "IGHV3-11*04": 0.0023088224744128587, "IGHV3-7*05": 2.138885549689037e-06}, "d_per_gene_support": {"IGHD6-6*01": 0.9665290028456096, "IGHD6-13*01": 0.03345580473895684, "IGHD1-26*01": 1.4749786163602158e-05, "IGHD6-19*01": 4.237301713307103e-07, "IGHD4-4*01": 1.8899053931530826e-08}, "j_per_gene_support": {"IGHJ4*02": 0.9999993846481249, "IGHJ5*02": 6.153518521915327e-07}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 6, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TATCCTAGAGGACTC", "dj_insertion": "CCTACCCTC", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 342}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-60/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-60/igh.fa new file mode 100644 index 000000000..37788832c --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-60/igh.fa @@ -0,0 +1,12 @@ +>901.d0 +GAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGATAAGGAGGCGGGGGCAGCTCGTCCGGACTTTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG +>06-B-M_2962542 +CATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATATATTTCTGTGCGAAACGAGAGGGGCAGCTCTCTTTCTACGCCCCCTCTACTGCTTTTAATATGTGGGGCCAGGGG +>-4847562276697408608 +CAGGTGCAGCTGGTGCAGTCTGGGTCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAAGCTTCTGGATACACCTTGAACGGCTATTACATGCACTGGGTGCGGCAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCATAAACTATGCGCAGAAGTTTCAGGGCAGCGTCACCATGACCAGGGACACGTCCGTCACCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGTCGACACGGCCGTATATTACTGTGGGAGAGCAGCATATTGTGGTGGCGACTACTGTTTTACTGAATACTTCCAGCACTGGGGCCAGGGCACCCCGGTCACCGTCTCTTCAG +>-9140119851721454527 +CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGGTCAACCCTAACAGTGGTGGCATAAACTATGCACAGAAGTTCCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAACAGGCTGAGATCTGTCGACACGGCCGTGTATTACTGTGCGAGAGTAGGATATTGTAGTGGTGGTAGCTGCTACGACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG +>-2746509048448212099 +CAGGTGCAGCTGCAATAGCCGGGCCCAAAACTTGCGAAGACTTCGCACACCCTGTCCCTCACCTGCGCTGTCCTCGATGGCTCCGTCAGCGCTGGTGGTTACTATTGAAGCCAGGCCCGCCAGCCTTCAGGGACGGGAGTAGACTGGATTGGGTGTATCTATTACAGTGCAAGCACCATCTACAAGCTCTCTCTCCATACTCGGGTTGCCATTTCTATCGACATGTCCAAGAGGCGGTTTTCACTGATTCTGACCTGGGTGACCGCAACCTACACGGCCGTTTATTACTGTGCGAAAAAGTGGTGCTATGATTGGAGCGTATAGGTCTCCGTTTTCGTAGTGCCGTGGGGACAGGGGACACTGGTCACCGTCTTCTCAG +>02-C-M_3281471 +CAAGAACTCACTGTATCTGCAAATGAACAGCCTGCGACCCGAGGACTCGGCTGTGTATTACTGTGCGCGAGACATTTTTTACGAGTCTTGGAGTGGTTTGAGTAACGGTATGGACGCCTGGGGCCAAGGG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-60/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-60/partition-igh.yaml new file mode 100644 index 000000000..966f02e12 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-60/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -1814.193384536927, "n_clusters": 6, "n_procs": 1, "partition": [["-2746509048448212099"], ["-4847562276697408608"], ["-9140119851721454527"], ["02-C-M_3281471"], ["06-B-M_2962542"], ["901.d0"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["-2746509048448212099"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 60, "mature_cdr3_lengths": [60], "mut_freqs": [0.24010554089709762], "n_mutations": 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["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGATAAGGAGGCGGGGGCAGCTCGTCCGGACTTTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG"], "naive_seq": "NNNNNNGAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGATAAGGAGGCGGGGGCAGCTCGTCCGGACTTTGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-69-1*02": 0.996132018475668, "IGHV3-11*04": 0.0038398058194565256, "IGHV3-66*02": 2.817570484947806e-05}, "d_per_gene_support": {"IGHD6-6*01": 0.9999158359276761, "IGHD6-13*01": 8.406929425235847e-05, "IGHD2-15*01": 9.471976302945949e-08, "IGHD2-21*02": 5.7778627930586256e-11, "IGHD5-5*01": 5.657963610287914e-13}, "j_per_gene_support": {"IGHJ3*02": 1.0}, "v_3p_del": 0, "d_5p_del": 7, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TAAGGAGGCGGGG", "dj_insertion": "GGACTT", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 345}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-63/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-63/igh.fa new file mode 100644 index 000000000..f28da00a2 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-63/igh.fa @@ -0,0 +1,2 @@ +>02-C-M_1115713 +GAACACACTGTATCTGCACATGGACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGATCTAAGAGTAGCTGGTATGTCGACCCGCCTCGGTCGGGGTATGGACGTCTGGGGCCAAGGG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-63/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-63/partition-igh.yaml new file mode 100644 index 000000000..05958f3e5 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-63/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -429.33092327968967, "n_clusters": 1, "n_procs": 1, "partition": [["02-C-M_1115713"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["02-C-M_1115713"], "invalid": false, "v_gene": "IGHV3-7*05", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ6*02", "cdr3_length": 63, "mature_cdr3_lengths": [63], "mut_freqs": [0.038461538461538464], "n_mutations": [5], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGAACACACTGTATCTGCACATGGACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGATCTAAGAGTAGCTGGTATGTCGACCCGCCTCGGTCGGGGTATGGACGTCTGGGGCCAAGGGNNNNNNNNNNNNNNNNNNNNNN"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGATCTAAGAGCAGCTGGTACGTCGACCCGCCTCGGTCGGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-7*05": 0.9397354595846363, "IGHV3-11*04": 0.06018465440974571, "IGHV3-69-1*02": 7.988600561350021e-05}, "d_per_gene_support": {"IGHD6-13*01": 0.939831768420429, "IGHD2-15*01": 0.035303739369688045, "IGHD6-19*01": 0.015000715342746525, "IGHD2-2*01": 0.0072951437676786616, "IGHD6-6*01": 0.002568633099410464}, "j_per_gene_support": {"IGHJ6*02": 0.9999999992241442, "IGHJ6*03": 7.758576907468156e-10}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 17, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TCTAAG", "dj_insertion": "GTCGACCCGCCTCGGTCGG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 345}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-66/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-66/igh.fa new file mode 100644 index 000000000..e65f1aa76 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-66/igh.fa @@ -0,0 +1,2 @@ +>04-A-M_2148159 +CCAGGTGGTCCTTACAGTGACCAACATGGATCCTGTGGACACAGGCACATATTACTGTGCACACACCTCTGTTCGGAATCATTTTCTTCGGGGAGTCATTATCGACCCACCTGACTTCTGGGGCCAGGGA diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-66/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-66/partition-igh.yaml new file mode 100644 index 000000000..e404a4cc9 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-66/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -447.48033223053835, "n_clusters": 1, "n_procs": 1, "partition": [["04-A-M_2148159"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["04-A-M_2148159"], "invalid": false, "v_gene": "IGHV2-5*02", "d_gene": "IGHD3-10*01", "j_gene": "IGHJ4*02", "cdr3_length": 66, "mature_cdr3_lengths": [66], "mut_freqs": [0.038461538461538464], "n_mutations": [5], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCCAGGTGGTCCTTACAGTGACCAACATGGATCCTGTGGACACAGGCACATATTACTGTGCACACACCTCTGTTCGGAATCATTTTCTTCGGGGAGTCATTATCGACCCACCTGACTTCTGGGGCCAGGGANNNNNNNNNNNNNNNNNNNNNN"], "naive_seq": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACACCTCTGTTCGGAATCATTTTCTTCGGGGAGTTATTATCGACCCACCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV2-5*02": 0.9999211699141256, "IGHV2-70D*04": 7.883008590104688e-05}, "d_per_gene_support": {"IGHD3-10*01": 0.9990604249838381, "IGHD3-10*03": 0.0009374088638921588, "IGHD1-26*01": 1.4370976247239868e-06, "IGHD3-16*02": 7.260869839513148e-07, "IGHD3-3*01": 2.9676987482946464e-09}, "j_per_gene_support": {"IGHJ4*02": 0.9999171422156304, "IGHJ5*02": 8.285778436132284e-05}, "v_3p_del": 3, "d_5p_del": 12, "d_3p_del": 3, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCTCTGTTCGGAATCATTTTC", "dj_insertion": "CGACCCACC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 288, "j": 351}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-71/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-71/igh.fa new file mode 100644 index 000000000..9db63af4b --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-71/igh.fa @@ -0,0 +1,2 @@ +>06-B-M_0345150 +TCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGTAACCCGTATTGTAGTGGTGGTAGCTGCTACCCTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-71/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-71/partition-igh.yaml new file mode 100644 index 000000000..3e5d0ba64 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-71/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -411.72633773029344, "n_clusters": 1, "n_procs": 1, "partition": [["06-B-M_0345150"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["06-B-M_0345150"], "invalid": false, "v_gene": "IGHV4-4*09", "d_gene": "IGHD2-15*01", "j_gene": "IGHJ6*03", "cdr3_length": 71, "mature_cdr3_lengths": [71], "mut_freqs": [0.007692307692307693], "n_mutations": [1], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCTGTGTATTACTGTGCGAGTAACCCGTATTGTAGTGGTGGTAGCTGCTACCCTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGNNNNNNNNNNNNNNNNNNNNNN"], "naive_seq": "NNNNNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTAACCCGTATTGTAGTGGTGGTAGCTGCTACCCTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-4*09": 0.8330856130294885, "IGHV4-34*01": 0.166844862506373, "IGHV4-61*01": 6.952446413770171e-05}, "d_per_gene_support": {"IGHD2-15*01": 0.9999999999945999, "IGHD2-8*02": 3.6731151469964325e-12, "IGHD2-2*01": 1.7135634925038433e-12}, "j_per_gene_support": {"IGHJ6*03": 0.9999999988458512, "IGHJ6*02": 1.1541323341201865e-09}, "v_3p_del": 3, "d_5p_del": 4, "d_3p_del": 3, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TAACCCG", "dj_insertion": "CC", "fv_insertion": "NNNNNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [false], "codon_positions": {"v": 288, "j": 356}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-73/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-73/igh.fa new file mode 100644 index 000000000..8a84d86c0 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-73/igh.fa @@ -0,0 +1,2 @@ +>02-C-M_0360936 +TATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGATTTAGCCCCTTCTAGTTCGGCATATTGTGGTGGTGCCCGAAGATAACTGGTTCGACCCCTGGGGCCAGGGA diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-73/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-73/partition-igh.yaml new file mode 100644 index 000000000..efca30814 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-73/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -429.0850768123627, "n_clusters": 1, "n_procs": 1, "partition": [["02-C-M_0360936"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["02-C-M_0360936"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD2-21*01", "j_gene": "IGHJ5*02", "cdr3_length": 73, "mature_cdr3_lengths": [73], "mut_freqs": [0.0], "n_mutations": [0], "input_seqs": ["NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGATTTAGCCCCTTCTAGTTCGGCATATTGTGGTGGTGCCCGAAGATAACTGGTTCGACCCCTGGGGCCAGGGANNNNNNNNNNNNNNNNNNNNNN"], "naive_seq": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGATTTAGCCCCTTCTAGTTCGGCATATTGTGGTGGTGCCCGAAGATAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-23*01": 0.9999973315443432, "IGHV3-7*05": 2.6157945367298426e-06, "IGHV3-11*04": 5.266110663093339e-08}, "d_per_gene_support": {"IGHD2-21*01": 0.9998865830519467, "IGHD2-21*02": 9.828713410250113e-05, "IGHD2-15*01": 1.4481111348276957e-05, "IGHD2-8*02": 6.482791648708485e-07, "IGHD2-2*01": 4.234166542785754e-10}, "j_per_gene_support": {"IGHJ5*02": 1.0}, "v_3p_del": 0, "d_5p_del": 1, "d_3p_del": 11, "j_5p_del": 2, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTTAGCCCCTTCTAGTTCG", "dj_insertion": "CCCGAAGAT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [true], "codon_positions": {"v": 285, "j": 355}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-81/igh.fa b/test/ref-results/disjoint-group-new-data/groups/cdr3-81/igh.fa new file mode 100644 index 000000000..82859f5cc --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-81/igh.fa @@ -0,0 +1,6 @@ +>6731449281791440313 +CAGGTACGTTTATCACAATTTGGGCCCTAGATCAAGAGGCCTGGGACGTCAGTGGTTGTCTCCTGCGAGACTTCTGAATAAACCTTTATTGACCGCTTTATACAATGGTTTCGACAGGCCCCAGGGCGATCCCTTGAGTGGATGGGATGGATCAATCCTGATAGCGGTGGAATTAACTTTCCATTGACCTTGCGGGGCACCATTGCCATGATCGCCGACACGGCTGTGAACACAGCTTATATGGTACTGAGTAGCTTGAGCTCTGACGACACGGCCCCCTACTACTGTGTGGGAGCCTCACGTTTGATCCCGAGTGGAGGGTTTGGTTTTATAACCACTTGCTACTATTGGTTTTTTGCTCCCTGGGGCCGCGGGCCCCTGGTCACCGTCTCCTCAG +>6785281000938532760 +CAGGTCCGGGTGGTGCAGTCTGGGGCTTAGTTTAAAAGACCTGGGGCCTCAGTGACGGTCTCATGCGTGACCTCTGGATATGTCTTCACCGACCAATTTATCTAGTGGGTGCGACAGGTCCATGGATAAGATCTTGGGTGGGTGGGGGGGATCAATCCTAAGAGTGGCGGTAGGAATTATGCATAGACCTTTCAACGCTCAGTCACCATCTACAGGGATCCGTCGACATGCACAGCCTAGGTGGAGCTTAGCACCCTGATATCTGAGGACACGGCCATGTATTACTGTGTGAGTGGAATGTATTGTTGTAGTGGTGCTCGCCATTCCAAGATAAGGATGTTTGATAAGTACTTATTTGGTTGGTGGGGCCCGGGAGCCCTGGTCCCCGTCTCCCCAG +>-991144955841202245 +CAGGTCCAGGTGGTGCAGTCTGGAGCTGAGGTCAAGACTCCTGGGGCCTCAGTGAAGATTTCTTGCAGGGCTTCTGGATACCCTTTCATTGAGTACTATATACACTGGGTGCGTCACGTCCTTGGACAGGACCTTGAGTGGGTGGGGTGGATCAATCCTTGCGGTGGTGGCACAAATTATGCCCACACGTTTCAAGGCAGAGTCACCATGATATGGGCCACCTCGGACAGCACAGCCTACATGGGCCTTAGCAGTCTGAGATCTGACGACACGGCCACGTATTACTGTGCAGGACGAGAGTGTAGTGTTGGTGGTCGCTACCAGTCCAAGATAAAGATGTTTGATAAGTAATCTACTGGAGGCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCCG diff --git a/test/ref-results/disjoint-group-new-data/groups/cdr3-81/partition-igh.yaml b/test/ref-results/disjoint-group-new-data/groups/cdr3-81/partition-igh.yaml new file mode 100644 index 000000000..b5cab82ec --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/groups/cdr3-81/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV1-2*02": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV2-5*02": "CAGATCACCTTGAAGGAGTCTGGTCCTACGCTGGTGAAACCCACACAGACCCTCACGCTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAGTGGGTGTGGGCTGGATCCGTCAGCCCCCAGGAAAGGCCCTGGAGTGGCTTGCACTCATTTATTGGGATGATGATAAGCGCTACAGCCCATCTCTGAAGAGCAGGCTCACCATCACCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACATATTACTGTGCACACAGAC", "IGHV2-70D*04": "CAGGTCACCTTGAAGGAGTCTGGTCCTGCGCTGGTGAAACCCACACAGACCCTCACACTGACCTGCACCTTCTCTGGGTTCTCACTCAGCACTAGTGGAATGCGTGTGAGCTGGATCCGTCAGCCCCCAGGGAAGGCCCTGGAGTGGCTTGCACGCATTGATTGGGATGATGATAAATTCTACAGCACATCTCTGAAGACCAGGCTCACCATCTCCAAGGACACCTCCAAAAACCAGGTGGTCCTTACAATGACCAACATGGACCCTGTGGACACAGCCACGTATTACTGTGCACGGATAC", "IGHV3-11*04": "CAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCAAGCCTGGAGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAGCTGGATCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTTTCATACATTAGTAGTAGTGGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGGGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-69-1*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTAAAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTCAGTGACTACTACATGAACTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCATCCATTAGTAGTAGTAGTACCATATACTACGCAGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCTGTTTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-9*02": "GAAGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGCAGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTCTGATGATTATGCCATGCACTGGGTCCGGCAAGCTCCAGGGAAGGGCCTGGAGTGGGTCTCAGGTATTAGTTGGAATAGTGGTAGCATAGGCTATGCGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCCCTGTATCTGCAAATGAACAGTCTGAGAGCTGAGGACACGGCCTTGTATTACTGTGCAAAAGATA", "IGHV4-34*01": "CAGGTGCAGCTACAGCAGTGGGGCGCAGGACTGTTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCGCTGTCTATGGTGGGTCCTTCAGTGGTTACTACTGGAGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGGAAATCAATCATAGTGGAAGCACCAACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCGGACACGGCTGTGTATTACTGTGCGAGAGG", "IGHV4-39*09": "CAGCTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGCAGTAGTAGTTACTACTGGGGCTGGATCCGCCAGCCCCCAGGGAAGGGGCTGGAGTGGATTGGGAGTATCTATTATAGTGGGAGCACCTACTACAACCCGTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCAGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD1-26*01": "GGTATAGTGGGAGCTACTAC", "IGHD2-15*01": "AGGATATTGTAGTGGTGGTAGCTGCTACTCC", "IGHD2-2*01": "AGGATATTGTAGTAGTACCAGCTGCTATGCC", "IGHD2-21*01": "AGCATATTGTGGTGGTGATTGCTATTCC", "IGHD2-21*02": "AGCATATTGTGGTGGTGACTGCTATTCC", "IGHD2-8*01": "AGGATATTGTACTAATGGTGTATGCTATACC", "IGHD2-8*02": "AGGATATTGTACTGGTGGTGTATGCTATACC", "IGHD3-10*01": "GTATTACTATGGTTCGGGGAGTTATTATAAC", "IGHD3-10*03": "GTATTACTATGGTTCAGGGAGTTATTATAAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD3-3*01": "GTATTACGATTTTTGGAGTGGTTATTATACC", "IGHD4-17*01": "TGACTACGGTGACTAC", "IGHD4-4*01": "TGACTACAGTAACTAC", "IGHD5-5*01": "GTGGATACAGCTATGGTTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC", "IGHD6-6*01": "GAGTATAGCAGCTCGTCC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ2*01": "CTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "IGHJ3*02": "TGATGCTTTTGATATCTGGGGCCAAGGGACAATGGTCACCGTCTCTTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ5*02": "ACAACTGGTTCGACCCCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "IGHJ6*03": "ATTACTACTACTACTACTACATGGACGTCTGGGGCAAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV2-5*02": 288, "IGHV4-34*01": 282, "IGHV1-2*02": 285, "IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV3-69-1*02": 282, "IGHV3-11*04": 285, "IGHV2-70D*04": 288, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV4-39*09": 288, "IGHV3-9*02": 285, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ2*01": 19, "IGHJ3*02": 16, "IGHJ6*02": 29, "IGHJ5*02": 17, "IGHJ1*01": 18, "IGHJ6*03": 29}}, "partitions": [{"logprob": -981.1416743615067, "n_clusters": 3, "n_procs": 1, "partition": [["-991144955841202245"], ["6731449281791440313"], ["6785281000938532760"]]}, {"logprob": -949.1360800306993, "n_clusters": 2, "n_procs": 1, "partition": [["-991144955841202245", "6785281000938532760"], ["6731449281791440313"]]}], "events": [{"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["-991144955841202245", "6785281000938532760"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD2-15*01", "j_gene": "IGHJ4*02", "cdr3_length": 81, "mature_cdr3_lengths": [81, 81], "mut_freqs": [0.18639798488664988, 0.22418136020151133], "n_mutations": [74, 89], "input_seqs": ["CAGGTCCAGGTGGTGCAGTCTGGAGCTGAGGTCAAGACTCCTGGGGCCTCAGTGAAGATTTCTTGCAGGGCTTCTGGATACCCTTTCATTGAGTACTATATACACTGGGTGCGTCACGTCCTTGGACAGGACCTTGAGTGGGTGGGGTGGATCAATCCTTGCGGTGGTGGCACAAATTATGCCCACACGTTTCAAGGCAGAGTCACCATGATATGGGCCACCTCGGACAGCACAGCCTACATGGGCCTTAGCAGTCTGAGATCTGACGACACGGCCACGTATTACTGTGCAGGACGAGAGTGTAGTGTTGGTGGTCGCTACCAGTCCAAGATAAAGATGTTTGATAAGTAATCTACTGGAGGCTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCCG", "CAGGTCCGGGTGGTGCAGTCTGGGGCTTAGTTTAAAAGACCTGGGGCCTCAGTGACGGTCTCATGCGTGACCTCTGGATATGTCTTCACCGACCAATTTATCTAGTGGGTGCGACAGGTCCATGGATAAGATCTTGGGTGGGTGGGGGGGATCAATCCTAAGAGTGGCGGTAGGAATTATGCATAGACCTTTCAACGCTCAGTCACCATCTACAGGGATCCGTCGACATGCACAGCCTAGGTGGAGCTTAGCACCCTGATATCTGAGGACACGGCCATGTATTACTGTGTGAGTGGAATGTATTGTTGTAGTGGTGCTCGCCATTCCAAGATAAGGATGTTTGATAAGTACTTATTTGGTTGGTGGGGCCCGGGAGCCCTGGTCCCCGTCTCCCCAG"], "naive_seq": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGGAGGATATTGTAGTGGTGGTAGCTGCTACTCCAAGATAAGGATGTTTGATAAGTACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD2-15*01": 0.9988674740242773, "IGHD2-21*01": 0.0009461294416576978, "IGHD2-8*01": 0.00014064590085212015, "IGHD2-21*02": 3.0139342864684957e-05, "IGHD2-8*02": 1.561129030831755e-05}, "j_per_gene_support": {"IGHJ4*02": 0.9999999761320172, "IGHJ5*02": 2.3867932296569936e-08}, "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "G", "dj_insertion": "AAGATAAGGATGTTTGATAAGT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [true, true], "codon_positions": {"v": 285, "j": 363}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["6731449281791440313"], "invalid": false, "v_gene": "IGHV1-2*02", "d_gene": "IGHD3-16*02", "j_gene": "IGHJ2*01", "cdr3_length": 81, "mature_cdr3_lengths": [81], "mut_freqs": [0.2795969773299748], "n_mutations": [111], "input_seqs": ["CAGGTACGTTTATCACAATTTGGGCCCTAGATCAAGAGGCCTGGGACGTCAGTGGTTGTCTCCTGCGAGACTTCTGAATAAACCTTTATTGACCGCTTTATACAATGGTTTCGACAGGCCCCAGGGCGATCCCTTGAGTGGATGGGATGGATCAATCCTGATAGCGGTGGAATTAACTTTCCATTGACCTTGCGGGGCACCATTGCCATGATCGCCGACACGGCTGTGAACACAGCTTATATGGTACTGAGTAGCTTGAGCTCTGACGACACGGCCCCCTACTACTGTGTGGGAGCCTCACGTTTGATCCCGAGTGGAGGGTTTGGTTTTATAACCACTTGCTACTATTGGTTTTTTGCTCCCTGGGGCCGCGGGCCCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGGTGCAGTCTGGGGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGATACACCTTCACCGGCTACTATATGCACTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAACCCTAACAGTGGTGGCACAAACTATGCACAGAAGTTTCAGGGCAGGGTCACCATGACCAGGGACACGTCCATCAGCACAGCCTACATGGAGCTGAGCAGGCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGCCTCTATTATGATTACGTTTGGGGGAGTTATCGTTATACCCACTTGCTACTACTGGTACTTCGATCTCTGGGGCCGTGGCACCCTGGTCACTGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV1-2*02": 1.0}, "d_per_gene_support": {"IGHD3-16*02": 0.9987538273554004, "IGHD3-10*01": 0.0010597609133278672, "IGHD3-3*01": 0.00015493684901680933, "IGHD3-10*03": 2.7944869091372347e-05, "IGHD2-2*01": 3.5300131925369885e-06}, "j_per_gene_support": {"IGHJ2*01": 0.9681570096629031, "IGHJ6*02": 0.03184299033709544}, "v_3p_del": 1, "d_5p_del": 1, "d_3p_del": 0, "j_5p_del": 0, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCTC", "dj_insertion": "CACTTGCTA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [true], "codon_positions": {"v": 285, "j": 363}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-data/manifest.yaml b/test/ref-results/disjoint-group-new-data/manifest.yaml new file mode 100644 index 000000000..2dc783e10 --- /dev/null +++ b/test/ref-results/disjoint-group-new-data/manifest.yaml @@ -0,0 +1,108 @@ +assembly: + merged_output_path: assembled/ + status: merged + validation: + gene_lists_consistent: null + sequence_count_preserved: true + uids_unique: true +grouping-info: + failed_sequences: 0 + loci: + - igh + method: cdr3-length + parameter_dir: test/ref-results/test/parameters/data + total_grouped_sequences: 46 + total_input_sequences: 46 +groups: +- cdr3_length: 32 + fasta_path: groups/cdr3-32/igh.fa + group_id: 0 + locus: igh + partition_path: groups/cdr3-32/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 33 + fasta_path: groups/cdr3-33/igh.fa + group_id: 1 + locus: igh + partition_path: groups/cdr3-33/partition-igh.yaml + sequence_count: 5 +- cdr3_length: 39 + fasta_path: groups/cdr3-39/igh.fa + group_id: 2 + locus: igh + partition_path: groups/cdr3-39/partition-igh.yaml + sequence_count: 3 +- cdr3_length: 42 + fasta_path: groups/cdr3-42/igh.fa + group_id: 3 + locus: igh + partition_path: groups/cdr3-42/partition-igh.yaml + sequence_count: 4 +- cdr3_length: 45 + fasta_path: groups/cdr3-45/igh.fa + group_id: 4 + locus: igh + partition_path: groups/cdr3-45/partition-igh.yaml + sequence_count: 4 +- cdr3_length: 48 + fasta_path: groups/cdr3-48/igh.fa + group_id: 5 + locus: igh + partition_path: groups/cdr3-48/partition-igh.yaml + sequence_count: 4 +- cdr3_length: 51 + fasta_path: groups/cdr3-51/igh.fa + group_id: 6 + locus: igh + partition_path: groups/cdr3-51/partition-igh.yaml + sequence_count: 2 +- cdr3_length: 54 + fasta_path: groups/cdr3-54/igh.fa + group_id: 7 + locus: igh + partition_path: groups/cdr3-54/partition-igh.yaml + sequence_count: 5 +- cdr3_length: 57 + fasta_path: groups/cdr3-57/igh.fa + group_id: 8 + locus: igh + partition_path: groups/cdr3-57/partition-igh.yaml + sequence_count: 5 +- cdr3_length: 60 + fasta_path: groups/cdr3-60/igh.fa + group_id: 9 + locus: igh + partition_path: groups/cdr3-60/partition-igh.yaml + sequence_count: 6 +- cdr3_length: 63 + fasta_path: groups/cdr3-63/igh.fa + group_id: 10 + locus: igh + partition_path: groups/cdr3-63/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 66 + fasta_path: groups/cdr3-66/igh.fa + group_id: 11 + locus: igh + partition_path: groups/cdr3-66/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 71 + fasta_path: groups/cdr3-71/igh.fa + group_id: 12 + locus: igh + partition_path: groups/cdr3-71/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 73 + fasta_path: groups/cdr3-73/igh.fa + group_id: 13 + locus: igh + partition_path: groups/cdr3-73/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 81 + fasta_path: groups/cdr3-81/igh.fa + group_id: 14 + locus: igh + partition_path: groups/cdr3-81/partition-igh.yaml + sequence_count: 3 +version-info: + partis-yaml: 0.2 diff --git a/test/ref-results/disjoint-group-new-simu/assembled/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/assembled/partition-igh.yaml new file mode 100644 index 000000000..da8ee23fe --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/assembled/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": 0.0, "n_clusters": 10, "n_procs": 1, "partition": [["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5", "9c3cedb840"], ["93c01dd961", "c761732a8b"], ["401a542698"], ["e64fcd9e03"], ["13de8675ec", "20a0129b57", "31e052ee14", "33aaa62e12", "4233d708fe", "91796617a0", "97366cf0d8"], ["188e1a0235", "226be79d5f"], ["adc41b4237"], ["162cb1691f", "17f57acf2e", "73431a9b10", "73d6c6e558", "948b83fb4d", "bf50fa2017", "c8a90cc3d7"], ["16df39683f", "7f6d2ba874", "6e208eca11"], ["d8761c689a"]]}], "events": [{"qr_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "gl_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "unique_ids": ["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5", "9c3cedb840"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33], "mut_freqs": [0.02023121387283237, 0.017341040462427744, 0.02023121387283237, 0.011560693641618497, 0.011560693641618497, 0.0, 0.0, 0.023121387283236993, 0.014450867052023121, 0.011560693641618497, 0.02023121387283237], "n_mutations": [7, 6, 7, 4, 4, 0, 0, 8, 5, 4, 7], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGACGGCTTGGTCCAGCCTGGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGGGCTGGGTCCGCCAGGCTCCAAGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTGAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTTTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTATCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGGGTATTACTGTGCGAGATCTATCGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCTTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTCGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGACACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCTGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACGTGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGTCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, false, false, false, false, false, false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999990460072187, "IGHD6-19*01": 9.533869768188863e-07, "IGHD1-20*01": 3.7711197600789503e-10, "IGHD3-22*01": 1.2948786393174627e-10, "IGHD3-16*02": 9.921291148651375e-11}, "j_per_gene_support": {"IGHJ4*02": 0.9999999996017834, "IGHJ1*01": 3.9821462372559203e-10}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, true, true], "stops": [true, true, true, true, true, false, false, true, true, true, true], "codon_positions": {"v": 282, "j": 312}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["93c01dd961", "c761732a8b"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD1-20*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39], "mut_freqs": [0.002840909090909091, 0.005681818181818182], "n_mutations": [1, 2], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACAAGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD1-20*01": 0.9823315087646157, "IGHD3-22*01": 0.015274256608703546, "IGHD6-13*01": 0.0022343398977644298, "IGHD3-16*02": 0.0001577327453410636, "IGHD6-19*01": 2.161983561188496e-06}, "j_per_gene_support": {"IGHJ4*02": 0.999999999884011, "IGHJ1*01": 1.1599442339996869e-10}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AGTATG", "dj_insertion": "TCTCAGA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 282, "j": 318}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["401a542698"], "invalid": false, "v_gene": "IGHV4-4*09", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.013850415512465374], "n_mutations": [5], "input_seqs": ["NNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTACTTACTACTGGAGCTGGATCCGGCAGTCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCAAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGTAGCAGAGCCCCTGTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "NNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGCAGCAGAGCCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-4*09": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999994128938585, "IGHD6-19*01": 3.9708495484223284e-07, "IGHD1-20*01": 1.895987979434448e-07, "IGHD3-22*01": 3.245194682080046e-10, "IGHD3-16*02": 9.786769630281464e-11}, "j_per_gene_support": {"IGHJ4*02": 0.9999984359791237, "IGHJ1*01": 1.564020882384402e-06}, "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 7, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTATTTGCTC", "dj_insertion": "AGCCCC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["e64fcd9e03"], "invalid": false, "v_gene": "IGHV5-51*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.01098901098901099], "n_mutations": [4], "input_seqs": ["GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGGGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTCTCCTGGTGACTCTGATGCCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGACTCCTCAG"], "has_shm_indels": [false], "naive_seq": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV5-51*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9816252648479535, "IGHD6-13*01": 0.01837473515204052}, "j_per_gene_support": {"IGHJ4*02": 0.9999999979584118, "IGHJ1*01": 2.0415837096006067e-09}, "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TA", "dj_insertion": "TCG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 330}}, {"qr_gap_seqs": ["", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGG...CTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGC.......TGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["13de8675ec", "20a0129b57", "31e052ee14", "33aaa62e12", "4233d708fe", "91796617a0", "97366cf0d8"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mature_cdr3_lengths": [51, 51, 51, 51, 51, 51, 51], "mut_freqs": [0.0, 0.0027247956403269754, 0.0, 0.0, 0.0, 0.0, 0.0027247956403269754], "n_mutations": [0, 1, 0, 0, 0, 0, 1], "input_seqs": ["CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTAGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTTCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, true, true, false, false, false], "naive_seq": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV1-18*01": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999941265543, "IGHD6-19*01": 5.826886624651332e-09, "IGHD1-20*01": 4.6561178291691886e-11, "IGHD3-16*02": 4.2604529547339967e-16, "IGHD3-22*01": 4.356768740429483e-18}, "j_per_gene_support": {"IGHJ4*02": 1.0, "IGHJ1*01": 5.970474439862842e-15}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 5, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCCTCGCA", "dj_insertion": "TCCCT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [false, false, false, false, false, false, false], "codon_positions": {"v": 285, "j": 333}}, {"qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["188e1a0235", "226be79d5f"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-16*02", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mature_cdr3_lengths": [54, 54], "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false], "naive_seq": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-23*01": 1.0}, "d_per_gene_support": {"IGHD3-16*02": 1.0}, "j_per_gene_support": {"IGHJ4*02": 0.9999999999969305, "IGHJ1*01": 3.0674025112535796e-12}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 285, "j": 336}}, {"qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["adc41b4237"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.013513513513513514], "n_mutations": [5], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTGCATGAGCTGGGTCCGCCAGGCTCCACGGGAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAAGACGCTGTATCTTCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999701819324, "IGHD3-16*02": 1.5755677982472836e-08, "IGHD6-19*01": 8.670260245537983e-09, "IGHD1-20*01": 5.030009169782335e-09, "IGHD3-22*01": 3.621418862900382e-10}, "j_per_gene_support": {"IGHJ4*02": 0.9999999892428947, "IGHJ1*01": 1.0757108869344984e-08}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 7, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTTTTGTGTCGGCAGGA", "dj_insertion": "GGCGCCC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 282, "j": 336}}, {"qr_gap_seqs": ["", "", "", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGT.......CTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATG.....AGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["", "", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["", "", "", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["162cb1691f", "17f57acf2e", "73431a9b10", "73d6c6e558", "948b83fb4d", "bf50fa2017", "c8a90cc3d7"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 60, "mature_cdr3_lengths": [60, 60, 60, 60, 60, 60, 60], "mut_freqs": [0.0158311345646438, 0.013192612137203167, 0.013192612137203167, 0.010554089709762533, 0.010554089709762533, 0.0079155672823219, 0.018469656992084433], "n_mutations": [6, 5, 5, 4, 4, 3, 7], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTAATACGAATACTTCCAGCACTGGGGCCAGGGCATCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGATTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGTACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAATTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGAGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAATCCTTCGGAGAGCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTAGTACAGTGGGAGCACCAACTACAACCCCTCCCTCAATAGTGGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCAGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false, true, false, false, false], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV4-61*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ1*01": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [true, true, false, false, false, false, true], "codon_positions": {"v": 288, "j": 345}}, {"qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["16df39683f", "7f6d2ba874", "6e208eca11"], "invalid": false, "v_gene": "IGHV3-7*05", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ6*02", "cdr3_length": 63, "mature_cdr3_lengths": [63, 63, 63], "mut_freqs": [0.0158311345646438, 0.010554089709762533, 0.023746701846965697], "n_mutations": [6, 4, 9], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTAAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGGGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGATCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATGTTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGCGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAAGGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCTAGAGACTGCGAAGCAGCTGGTACCTGTTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGACAAGGGACCACGGTCACCGTCTCCTCAG"], "has_shm_indels": [false, false, false], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV3-7*05": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.999999901643212, "IGHD6-19*01": 9.693287596401349e-08, "IGHD1-20*01": 1.4239358155007022e-09, "IGHD3-16*02": 2.1167722175408345e-16, "IGHD3-22*01": 7.167685230294717e-20}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 17, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CTGCGA", "dj_insertion": "CTATTCTAAGTTGCGTGAG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [true, true, true], "codon_positions": {"v": 285, "j": 345}}, {"qr_gap_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACC............AGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["d8761c689a"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 64, "mature_cdr3_lengths": [64], "mut_freqs": [0.020887728459530026], "n_mutations": [8], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "has_shm_indels": [true], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-61*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ1*01": 0.9999368233115588, "IGHJ4*02": 6.317668843798185e-05}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GAATACT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [false], "codon_positions": {"v": 288, "j": 349}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-33/igh.fa b/test/ref-results/disjoint-group-new-simu/groups/cdr3-33/igh.fa new file mode 100644 index 000000000..85afce77d --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-33/igh.fa @@ -0,0 +1,22 @@ +>8024ed1a22 +GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>18f4019708 +GAGGTGCAGCTGGTGGAGTCTGGGGACGGCTTGGTCCAGCCTGGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG +>ee25049b92 +GAGGTGCAGCTCGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGACACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>efdea248af +GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCTGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACGTGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGTCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>5fb484a8a6 +GAGGTGCAGCTGGTGGAGTTTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTATCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGGGTATTACTGTGCGAGATCTATCGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCTTCTCCTCAG +>9c3cedb840 +GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>648902c3e5 +GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>f47122f1f5 +GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>308de1d739 +GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGGGCTGGGTCCGCCAGGCTCCAAGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTGAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>d024e5cab0 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>822801f8ab +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igh.yaml new file mode 100644 index 000000000..a741c3c77 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-33/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -503.55657685608014, "n_clusters": 2, "n_procs": 1, "partition": [["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5"], ["9c3cedb840"]]}, {"logprob": -486.544787908427, "n_clusters": 1, "n_procs": 1, "partition": [["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5", "9c3cedb840"]]}], "events": [{"has_shm_indels": [false, false, false, false, false, false, false, false, false, false, false], "qr_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "gl_gap_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "indel_reversed_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "unique_ids": ["18f4019708", "308de1d739", "5fb484a8a6", "648902c3e5", "8024ed1a22", "822801f8ab", "d024e5cab0", "ee25049b92", "efdea248af", "f47122f1f5", "9c3cedb840"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 33, "mature_cdr3_lengths": [33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33], "mut_freqs": [0.02023121387283237, 0.017341040462427744, 0.02023121387283237, 0.011560693641618497, 0.011560693641618497, 0.0, 0.0, 0.023121387283236993, 0.014450867052023121, 0.011560693641618497, 0.02023121387283237], "n_mutations": [7, 6, 7, 4, 4, 0, 0, 8, 5, 4, 7], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGACGGCTTGGTCCAGCCTGGGGGGTGCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCTAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGCCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCGGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGGGCTGGGTCCGCCAGGCTCCAAGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTGAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTTTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTATCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGGGTATTACTGTGCGAGATCTATCGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCTTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTCGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGACACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCTGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACGTGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGTCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAAAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTAAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTAATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGAAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTTTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTAAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCTTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCCATAGCAGCAGCCGACTTATGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGATCTATAGCAGCAGCCGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999990460072187, "IGHD6-19*01": 9.533869768188863e-07, "IGHD1-20*01": 3.7711197600789503e-10, "IGHD3-22*01": 1.2948786393174627e-10, "IGHD3-16*02": 9.921291148651375e-11}, "j_per_gene_support": {"IGHJ4*02": 0.9999999996017834, "IGHJ1*01": 3.9821462372559203e-10}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TC", "dj_insertion": "C", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true, true, true, true, true], "stops": [true, true, true, true, true, false, false, true, true, true, true], "codon_positions": {"v": 282, "j": 312}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-39/igh.fa b/test/ref-results/disjoint-group-new-simu/groups/cdr3-39/igh.fa new file mode 100644 index 000000000..7c6309f4c --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-39/igh.fa @@ -0,0 +1,4 @@ +>93c01dd961 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>c761732a8b +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACAAGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-39/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/groups/cdr3-39/partition-igh.yaml new file mode 100644 index 000000000..0abec188c --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-39/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -100.48544705416865, "n_clusters": 1, "n_procs": 1, "partition": [["93c01dd961", "c761732a8b"]]}], "events": [{"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["93c01dd961", "c761732a8b"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD1-20*01", "j_gene": "IGHJ4*02", "cdr3_length": 39, "mature_cdr3_lengths": [39, 39], "mut_freqs": [0.002840909090909091, 0.005681818181818182], "n_mutations": [1, 2], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACAAGGCTGTGGATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAAGTATGATAACTGGTCTCAGAGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD1-20*01": 0.9823315087646157, "IGHD3-22*01": 0.015274256608703546, "IGHD6-13*01": 0.0022343398977644298, "IGHD3-16*02": 0.0001577327453410636, "IGHD6-19*01": 2.161983561188496e-06}, "j_per_gene_support": {"IGHJ4*02": 0.999999999884011, "IGHJ1*01": 1.1599442339996869e-10}, "v_3p_del": 2, "d_5p_del": 3, "d_3p_del": 6, "j_5p_del": 8, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "AGTATG", "dj_insertion": "TCTCAGA", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 282, "j": 318}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-48/igh.fa b/test/ref-results/disjoint-group-new-simu/groups/cdr3-48/igh.fa new file mode 100644 index 000000000..8e7bb2dea --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-48/igh.fa @@ -0,0 +1,4 @@ +>401a542698 +CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTACTTACTACTGGAGCTGGATCCGGCAGTCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCAAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGTAGCAGAGCCCCTGTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>e64fcd9e03 +GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGGGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTCTCCTGGTGACTCTGATGCCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGACTCCTCAG diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-48/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/groups/cdr3-48/partition-igh.yaml new file mode 100644 index 000000000..5d9073ba1 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-48/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -203.16431346741814, "n_clusters": 2, "n_procs": 1, "partition": [["401a542698"], ["e64fcd9e03"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["401a542698"], "invalid": false, "v_gene": "IGHV4-4*09", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.013850415512465374], "n_mutations": [5], "input_seqs": ["NNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTACTTACTACTGGAGCTGGATCCGGCAGTCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCAAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGTAGCAGAGCCCCTGTCTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "NNNCAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGTTATTTGCTCGGGTATAGCAGCAGAGCCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-4*09": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999994128938585, "IGHD6-19*01": 3.9708495484223284e-07, "IGHD1-20*01": 1.895987979434448e-07, "IGHD3-22*01": 3.245194682080046e-10, "IGHD3-16*02": 9.786769630281464e-11}, "j_per_gene_support": {"IGHJ4*02": 0.9999984359791237, "IGHJ1*01": 1.564020882384402e-06}, "v_3p_del": 3, "d_5p_del": 0, "d_3p_del": 7, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TTATTTGCTC", "dj_insertion": "AGCCCC", "fv_insertion": "NNN", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 330}}, {"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["e64fcd9e03"], "invalid": false, "v_gene": "IGHV5-51*01", "d_gene": "IGHD6-19*01", "j_gene": "IGHJ4*02", "cdr3_length": 48, "mature_cdr3_lengths": [48], "mut_freqs": [0.01098901098901099], "n_mutations": [4], "input_seqs": ["GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGGGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTCTCCTGGTGACTCTGATGCCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGACTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACTAGGGTATAGCAGTGGCTGGTACTCGTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV5-51*01": 1.0}, "d_per_gene_support": {"IGHD6-19*01": 0.9816252648479535, "IGHD6-13*01": 0.01837473515204052}, "j_per_gene_support": {"IGHJ4*02": 0.9999999979584118, "IGHJ1*01": 2.0415837096006067e-09}, "v_3p_del": 1, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "TA", "dj_insertion": "TCG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 285, "j": 330}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-51/igh.fa b/test/ref-results/disjoint-group-new-simu/groups/cdr3-51/igh.fa new file mode 100644 index 000000000..8c66c2908 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-51/igh.fa @@ -0,0 +1,14 @@ +>20a0129b57 +CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTAGTCACCGTCTCCTCAG +>91796617a0 +CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>4233d708fe +CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>97366cf0d8 +CAGGTTCAGCTGGTTCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>13de8675ec +CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>33aaa62e12 +CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>31e052ee14 +CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-51/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/groups/cdr3-51/partition-igh.yaml new file mode 100644 index 000000000..cf4012975 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-51/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -258.1592117240083, "n_clusters": 1, "n_procs": 1, "partition": [["13de8675ec", "20a0129b57", "31e052ee14", "33aaa62e12", "4233d708fe", "91796617a0", "97366cf0d8"]]}], "events": [{"has_shm_indels": [false, false, true, true, false, false, false], "qr_gap_seqs": ["", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGG...CTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGC.......TGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["", "", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["13de8675ec", "20a0129b57", "31e052ee14", "33aaa62e12", "4233d708fe", "91796617a0", "97366cf0d8"], "invalid": false, "v_gene": "IGHV1-18*01", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 51, "mature_cdr3_lengths": [51, 51, 51, 51, 51, 51, 51], "mut_freqs": [0.0, 0.0027247956403269754, 0.0, 0.0, 0.0, 0.0, 0.0027247956403269754], "n_mutations": [0, 1, 0, 0, 0, 0, 1], "input_seqs": ["CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTAGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGGACCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTAAGCTGTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "CAGGTTCAGCTGGTTCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGACCCCTCGCAGTATAGCAGCAGCTTCCCTTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV1-18*01": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999941265543, "IGHD6-19*01": 5.826886624651332e-09, "IGHD1-20*01": 4.6561178291691886e-11, "IGHD3-16*02": 4.2604529547339967e-16, "IGHD3-22*01": 4.356768740429483e-18}, "j_per_gene_support": {"IGHJ4*02": 1.0, "IGHJ1*01": 5.970474439862842e-15}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 5, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CCCCTCGCA", "dj_insertion": "TCCCT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [false, false, false, false, false, false, false], "codon_positions": {"v": 285, "j": 333}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-54/igh.fa b/test/ref-results/disjoint-group-new-simu/groups/cdr3-54/igh.fa new file mode 100644 index 000000000..d2f5873f8 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-54/igh.fa @@ -0,0 +1,4 @@ +>226be79d5f +GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG +>188e1a0235 +GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-54/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/groups/cdr3-54/partition-igh.yaml new file mode 100644 index 000000000..4aa28a4f9 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-54/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -85.71909844639075, "n_clusters": 1, "n_procs": 1, "partition": [["188e1a0235", "226be79d5f"]]}], "events": [{"has_shm_indels": [false, false], "qr_gap_seqs": ["", ""], "gl_gap_seqs": ["", ""], "indel_reversed_seqs": ["", ""], "unique_ids": ["188e1a0235", "226be79d5f"], "invalid": false, "v_gene": "IGHV3-23*01", "d_gene": "IGHD3-16*02", "j_gene": "IGHJ4*02", "cdr3_length": 54, "mature_cdr3_lengths": [54, 54], "mut_freqs": [0.0, 0.0], "n_mutations": [0, 0], "input_seqs": ["GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGAATTACGTTTGGGGGAGTTATCGTTATACCCCTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], []], "leader_seqs": ["", ""], "c_gene_seqs": ["", ""], "v_per_gene_support": {"IGHV3-23*01": 1.0}, "d_per_gene_support": {"IGHD3-16*02": 1.0}, "j_per_gene_support": {"IGHJ4*02": 0.9999999999969305, "IGHJ1*01": 3.0674025112535796e-12}, "v_3p_del": 0, "d_5p_del": 8, "d_3p_del": 0, "j_5p_del": 5, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "CC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false], "in_frames": [true, true], "stops": [false, false], "codon_positions": {"v": 285, "j": 336}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-57/igh.fa b/test/ref-results/disjoint-group-new-simu/groups/cdr3-57/igh.fa new file mode 100644 index 000000000..5ec7ebdaa --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-57/igh.fa @@ -0,0 +1,2 @@ +>adc41b4237 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTGCATGAGCTGGGTCCGCCAGGCTCCACGGGAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAAGACGCTGTATCTTCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-57/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/groups/cdr3-57/partition-igh.yaml new file mode 100644 index 000000000..ca9e2ec5c --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-57/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -103.88491914763259, "n_clusters": 1, "n_procs": 1, "partition": [["adc41b4237"]]}], "events": [{"has_shm_indels": [false], "qr_gap_seqs": [""], "gl_gap_seqs": [""], "indel_reversed_seqs": [""], "unique_ids": ["adc41b4237"], "invalid": false, "v_gene": "IGHV3-66*02", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ4*02", "cdr3_length": 57, "mature_cdr3_lengths": [57], "mut_freqs": [0.013513513513513514], "n_mutations": [5], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTGCATGAGCTGGGTCCGCCAGGCTCCACGGGAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAAGACGCTGTATCTTCAAATGAACAGCCTGAGACCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGAGTTTTGTGTCGGCAGGAGTATAGCAGCAGGGCGCCCTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV3-66*02": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.9999999701819324, "IGHD3-16*02": 1.5755677982472836e-08, "IGHD6-19*01": 8.670260245537983e-09, "IGHD1-20*01": 5.030009169782335e-09, "IGHD3-22*01": 3.621418862900382e-10}, "j_per_gene_support": {"IGHJ4*02": 0.9999999892428947, "IGHJ1*01": 1.0757108869344984e-08}, "v_3p_del": 0, "d_5p_del": 2, "d_3p_del": 7, "j_5p_del": 7, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "GTTTTGTGTCGGCAGGA", "dj_insertion": "GGCGCCC", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [true], "stops": [false], "codon_positions": {"v": 282, "j": 336}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-60/igh.fa b/test/ref-results/disjoint-group-new-simu/groups/cdr3-60/igh.fa new file mode 100644 index 000000000..b9a14ac66 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-60/igh.fa @@ -0,0 +1,14 @@ +>bf50fa2017 +CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG +>73d6c6e558 +CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG +>162cb1691f +CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTAATACGAATACTTCCAGCACTGGGGCCAGGGCATCCTGGTCACCGTCTCCTCAG +>c8a90cc3d7 +CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAATCCTTCGGAGAGCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTAGTACAGTGGGAGCACCAACTACAACCCCTCCCTCAATAGTGGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCAGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG +>17f57acf2e +CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGATTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG +>948b83fb4d +CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGAGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG +>73431a9b10 +CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGTACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAATTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-60/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/groups/cdr3-60/partition-igh.yaml new file mode 100644 index 000000000..ce2c3067e --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-60/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -410.64471854438085, "n_clusters": 1, "n_procs": 1, "partition": [["162cb1691f", "17f57acf2e", "73431a9b10", "73d6c6e558", "948b83fb4d", "bf50fa2017", "c8a90cc3d7"]]}], "events": [{"has_shm_indels": [false, false, false, true, false, false, false], "qr_gap_seqs": ["", "", "", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGT.......CTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATG.....AGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "gl_gap_seqs": ["", "", "", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "indel_reversed_seqs": ["", "", "", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "", "", ""], "unique_ids": ["162cb1691f", "17f57acf2e", "73431a9b10", "73d6c6e558", "948b83fb4d", "bf50fa2017", "c8a90cc3d7"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 60, "mature_cdr3_lengths": [60, 60, 60, 60, 60, 60, 60], "mut_freqs": [0.0158311345646438, 0.013192612137203167, 0.013192612137203167, 0.010554089709762533, 0.010554089709762533, 0.0079155672823219, 0.018469656992084433], "n_mutations": [6, 5, 5, 4, 4, 3, 7], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTAATACGAATACTTCCAGCACTGGGGCCAGGGCATCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTAGTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGATTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACACCCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGTACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAATTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGACTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGAGTGCTTACTACTACGAAGACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGAGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCTCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAGGAGGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAATCCTTCGGAGAGCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTAGTACAGTGGGAGCACCAACTACAACCCCTCCCTCAATAGTGGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCAGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[], [], [], [], [], [], []], "leader_seqs": ["", "", "", "", "", "", ""], "c_gene_seqs": ["", "", "", "", "", "", ""], "v_per_gene_support": {"IGHV4-61*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ1*01": 1.0}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 3, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false, false, false, false, false], "in_frames": [true, true, true, true, true, true, true], "stops": [true, true, false, false, false, false, true], "codon_positions": {"v": 288, "j": 345}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-63/igh.fa b/test/ref-results/disjoint-group-new-simu/groups/cdr3-63/igh.fa new file mode 100644 index 000000000..25b2aa913 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-63/igh.fa @@ -0,0 +1,6 @@ +>16df39683f +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTAAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGGGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGATCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG +>6e208eca11 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGCGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAAGGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCTAGAGACTGCGAAGCAGCTGGTACCTGTTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGACAAGGGACCACGGTCACCGTCTCCTCAG +>7f6d2ba874 +GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATGTTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-63/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/groups/cdr3-63/partition-igh.yaml new file mode 100644 index 000000000..5c0bbecac --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-63/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -333.61437327217607, "n_clusters": 2, "n_procs": 1, "partition": [["16df39683f", "7f6d2ba874"], ["6e208eca11"]]}, {"logprob": -285.6467094175916, "n_clusters": 1, "n_procs": 1, "partition": [["16df39683f", "7f6d2ba874", "6e208eca11"]]}], "events": [{"has_shm_indels": [false, false, false], "qr_gap_seqs": ["", "", ""], "gl_gap_seqs": ["", "", ""], "indel_reversed_seqs": ["", "", ""], "unique_ids": ["16df39683f", "7f6d2ba874", "6e208eca11"], "invalid": false, "v_gene": "IGHV3-7*05", "d_gene": "IGHD6-13*01", "j_gene": "IGHJ6*02", "cdr3_length": 63, "mature_cdr3_lengths": [63, 63, 63], "mut_freqs": [0.0158311345646438, 0.010554089709762533, 0.023746701846965697], "n_mutations": [6, 4, 9], "input_seqs": ["GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTAAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGGGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGATCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATGTTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGCGCAGCCTCTGGATTCACCTTTAGTAGCTAATGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAAGGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATATTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAAGACACGGCCGTGTATTACTGTGCTAGAGACTGCGAAGCAGCTGGTACCTGTTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGACAAGGGACCACGGTCACCGTCTCCTCAG"], "naive_seq": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGACTGCGAAGCAGCTGGTACCTATTCTAAGTTGCGTGAGGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG", "duplicates": [[], [], []], "leader_seqs": ["", "", ""], "c_gene_seqs": ["", "", ""], "v_per_gene_support": {"IGHV3-7*05": 1.0}, "d_per_gene_support": {"IGHD6-13*01": 0.999999901643212, "IGHD6-19*01": 9.693287596401349e-08, "IGHD1-20*01": 1.4239358155007022e-09, "IGHD3-16*02": 2.1167722175408345e-16, "IGHD3-22*01": 7.167685230294717e-20}, "j_per_gene_support": {"IGHJ6*02": 1.0}, "v_3p_del": 0, "d_5p_del": 9, "d_3p_del": 0, "j_5p_del": 17, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "CTGCGA", "dj_insertion": "CTATTCTAAGTTGCGTGAG", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false, false, false], "in_frames": [true, true, true], "stops": [true, true, true], "codon_positions": {"v": 285, "j": 345}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-64/igh.fa b/test/ref-results/disjoint-group-new-simu/groups/cdr3-64/igh.fa new file mode 100644 index 000000000..fbfaeba6b --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-64/igh.fa @@ -0,0 +1,2 @@ +>d8761c689a +CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG diff --git a/test/ref-results/disjoint-group-new-simu/groups/cdr3-64/partition-igh.yaml b/test/ref-results/disjoint-group-new-simu/groups/cdr3-64/partition-igh.yaml new file mode 100644 index 000000000..143ed9330 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/groups/cdr3-64/partition-igh.yaml @@ -0,0 +1 @@ +{"version-info": {"partis-yaml": 0.1, "partis-git": ""}, "germline-info": {"locus": "igh", "functionalities": {}, "seqs": {"v": {"IGHV1-18*01": "CAGGTTCAGCTGGTGCAGTCTGGAGCTGAGGTGAAGAAGCCTGGGGCCTCAGTGAAGGTCTCCTGCAAGGCTTCTGGTTACACCTTTACCAGCTATGGTATCAGCTGGGTGCGACAGGCCCCTGGACAAGGGCTTGAGTGGATGGGATGGATCAGCGCTTACAATGGTAACACAAACTATGCACAGAAGCTCCAGGGCAGAGTCACCATGACCACAGACACATCCACGAGCACAGCCTACATGGAGCTGAGGAGCCTGAGATCTGACGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV3-23*01": "GAGGTGCAGCTGTTGGAGTCTGGGGGAGGCTTGGTACAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGCAGCTATGCCATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGCTATTAGTGGTAGTGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGGTTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTATATTACTGTGCGAAAGA", "IGHV3-66*02": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCGTCAGTAGCAACTACATGAGCTGGGTCCGCCAGGCTCCAGGGAAGGGGCTGGAGTGGGTCTCAGTTATTTATAGCGGTGGTAGCACATACTACGCAGACTCCGTGAAGGGCCGATTCACCATCTCCAGAGACAATTCCAAGAACACGCTGTATCTTCAAATGAACAGCCTGAGAGCTGAGGACACGGCTGTGTATTACTGTGCGAGAGA", "IGHV3-7*05": "GAGGTGCAGCTGGTGGAGTCTGGGGGAGGCTTGGTCCAGCCTGGGGGGTCCCTGAGACTCTCCTGTGCAGCCTCTGGATTCACCTTTAGTAGCTATTGGATGAGCTGGGTCCGCCAGGCTCCAGGGAAAGGGCTGGAGTGGGTGGCCAACATAAAGCAAGATGGAAGTGAGAAATACTATGTGGACTCTGTGAAGGGCCGATTCACCATCTCCAGAGACAACGCCAAGAACTCACTGTATCTGCAAATGAACAGCCTGAGAGCCGAGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-4*09": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCATCAGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTACATCTATACCAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCCGCAGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV4-61*01": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGA", "IGHV5-51*01": "GAGGTGCAGCTGGTGCAGTCTGGAGCAGAGGTGAAAAAGCCCGGGGAGTCTCTGAAGATCTCCTGTAAGGGTTCTGGATACAGCTTTACCAGCTACTGGATCGGCTGGGTGCGCCAGATGCCCGGGAAAGGCCTGGAGTGGATGGGGATCATCTATCCTGGTGACTCTGATACCAGATACAGCCCGTCCTTCCAAGGCCAGGTCACCATCTCAGCCGACAAGTCCATCAGCACCGCCTACCTGCAGTGGAGCAGCCTGAAGGCCTCGGACACCGCCATGTATTACTGTGCGAGACA"}, "d": {"IGHD1-20*01": "GGTATAACTGGAACGAC", "IGHD3-16*02": "GTATTATGATTACGTTTGGGGGAGTTATCGTTATACC", "IGHD3-22*01": "GTATTACTATGATAGTAGTGGTTATTACTAC", "IGHD6-13*01": "GGGTATAGCAGCAGCTGGTAC", "IGHD6-19*01": "GGGTATAGCAGTGGCTGGTAC"}, "j": {"IGHJ1*01": "GCTGAATACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "IGHJ4*02": "ACTACTTTGACTACTGGGGCCAGGGAACCCTGGTCACCGTCTCCTCAG", "IGHJ6*02": "ATTACTACTACTACTACGGTATGGACGTCTGGGGCCAAGGGACCACGGTCACCGTCTCCTCAG"}}, "cyst-positions": {"IGHV1-18*01": 285, "IGHV3-7*05": 285, "IGHV5-51*01": 285, "IGHV3-66*02": 282, "IGHV3-23*01": 285, "IGHV4-61*01": 288, "IGHV4-4*09": 282}, "tryp-positions": {"IGHJ4*02": 14, "IGHJ6*02": 29, "IGHJ1*01": 18}}, "partitions": [{"logprob": -103.17011851541247, "n_clusters": 1, "n_procs": 1, "partition": [["d8761c689a"]]}], "events": [{"has_shm_indels": [true], "qr_gap_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACC............AGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "gl_gap_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "indel_reversed_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "unique_ids": ["d8761c689a"], "invalid": false, "v_gene": "IGHV4-61*01", "d_gene": "IGHD3-22*01", "j_gene": "IGHJ1*01", "cdr3_length": 64, "mature_cdr3_lengths": [64], "mut_freqs": [0.020887728459530026], "n_mutations": [8], "input_seqs": ["CAGGTGCAGCTGCAGGAGTCGGGACCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGATGCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGCTGAGCTCTGTGACCGCTGCGGACACGGCTGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTACTACTACGAATACTTCATTCCAGCACTGGAGCCAGGGCACCCTGGTCACCGTCTCCTCAG"], "naive_seq": "CAGGTGCAGCTGCAGGAGTCGGGCCCAGGACTGGTGAAGCCTTCGGAGACCCTGTCCCTCACCTGCACTGTCTCTGGTGGCTCCGTCAGCAGTGGTAGTTACTACTGGAGCTGGATCCGGCAGCCCCCAGGGAAGGGACTGGAGTGGATTGGGTATATCTATTACAGTGGGAGCACCAACTACAACCCCTCCCTCAAGAGTCGAGTCACCATATCAGTAGACACGTCCAAGAACCAGTTCTCCCTGAAGCTGAGCTCTGTGACCGCTGCGGACACGGCCGTGTATTACTGTGCGAGAGAGTATTACTATGATAGTAGTGGTTATTACTACGAATACTTACTTCCAGCACTGGGGCCAGGGCACCCTGGTCACCGTCTCCTCAG", "duplicates": [[]], "leader_seqs": [""], "c_gene_seqs": [""], "v_per_gene_support": {"IGHV4-61*01": 1.0}, "d_per_gene_support": {"IGHD3-22*01": 1.0}, "j_per_gene_support": {"IGHJ1*01": 0.9999368233115588, "IGHJ4*02": 6.317668843798185e-05}, "v_3p_del": 0, "d_5p_del": 0, "d_3p_del": 0, "j_5p_del": 6, "v_5p_del": 0, "j_3p_del": 0, "vd_insertion": "", "dj_insertion": "GAATACT", "fv_insertion": "", "jf_insertion": "", "mutated_invariants": [false], "in_frames": [false], "stops": [false], "codon_positions": {"v": 288, "j": 349}}]} \ No newline at end of file diff --git a/test/ref-results/disjoint-group-new-simu/manifest.yaml b/test/ref-results/disjoint-group-new-simu/manifest.yaml new file mode 100644 index 000000000..f3e0dc1f9 --- /dev/null +++ b/test/ref-results/disjoint-group-new-simu/manifest.yaml @@ -0,0 +1,72 @@ +assembly: + merged_output_path: assembled/ + status: merged + validation: + gene_lists_consistent: null + sequence_count_preserved: true + uids_unique: true +grouping-info: + failed_sequences: 0 + loci: + - igh + method: cdr3-length + parameter_dir: test/ref-results/test/parameters/simu + total_grouped_sequences: 36 + total_input_sequences: 36 +groups: +- cdr3_length: 33 + fasta_path: groups/cdr3-33/igh.fa + group_id: 0 + locus: igh + partition_path: groups/cdr3-33/partition-igh.yaml + sequence_count: 11 +- cdr3_length: 39 + fasta_path: groups/cdr3-39/igh.fa + group_id: 1 + locus: igh + partition_path: groups/cdr3-39/partition-igh.yaml + sequence_count: 2 +- cdr3_length: 48 + fasta_path: groups/cdr3-48/igh.fa + group_id: 2 + locus: igh + partition_path: groups/cdr3-48/partition-igh.yaml + sequence_count: 2 +- cdr3_length: 51 + fasta_path: groups/cdr3-51/igh.fa + group_id: 3 + locus: igh + partition_path: groups/cdr3-51/partition-igh.yaml + sequence_count: 7 +- cdr3_length: 54 + fasta_path: groups/cdr3-54/igh.fa + group_id: 4 + locus: igh + partition_path: groups/cdr3-54/partition-igh.yaml + sequence_count: 2 +- cdr3_length: 57 + fasta_path: groups/cdr3-57/igh.fa + group_id: 5 + locus: igh + partition_path: groups/cdr3-57/partition-igh.yaml + sequence_count: 1 +- cdr3_length: 60 + fasta_path: groups/cdr3-60/igh.fa + group_id: 6 + locus: igh + partition_path: groups/cdr3-60/partition-igh.yaml + sequence_count: 7 +- cdr3_length: 63 + fasta_path: groups/cdr3-63/igh.fa + group_id: 7 + locus: igh + partition_path: groups/cdr3-63/partition-igh.yaml + sequence_count: 3 +- cdr3_length: 64 + fasta_path: groups/cdr3-64/igh.fa + group_id: 8 + locus: igh + partition_path: groups/cdr3-64/partition-igh.yaml + sequence_count: 1 +version-info: + partis-yaml: 0.2 diff --git a/test/test.py b/test/test.py index d61433d88..a7357c86c 100755 --- a/test/test.py +++ b/test/test.py @@ -10,6 +10,7 @@ import math import shutil import time +import collections from collections import OrderedDict from subprocess import Popen, PIPE, check_call, check_output, CalledProcessError import copy @@ -210,10 +211,149 @@ def add_inference_tests(input_stype): # if input_stype is 'ref', infer on old s self.perf_info = {version_stype : {} for version_stype in self.stypes} + # ---------------------------------------------------------------------------------------- + def run_disjoint_group_tests(self, args): + # run the three-step disjoint grouping pipeline on test data + # tests both simulated (ground truth) and real (robustness) paired data + if args.dry_run or args.dont_run: + return + import partis.disjointgrouper as disjointgrouper + + test_configs = [] + if args.paired: + test_configs.append({ + 'name' : 'disjoint-group-new-simu', + 'paired_indir' : self.inpath('new' if args.bust_cache else 'ref', 'simu'), + 'parameter_dir' : self.paramdir('new' if args.bust_cache else 'ref', 'simu'), + 'is_simu' : True, + }) + test_configs.append({ + 'name' : 'disjoint-group-new-data', + 'paired_indir' : 'test/paired-data', + 'parameter_dir' : self.paramdir('new' if args.bust_cache else 'ref', 'data'), + 'is_simu' : False, + }) + else: + test_configs.append({ + 'name' : 'disjoint-group-new-simu', + 'infname' : self.inpath('new' if args.bust_cache else 'ref', 'simu'), + 'parameter_dir' : self.paramdir('new' if args.bust_cache else 'ref', 'simu'), + 'is_simu' : True, + }) + test_configs.append({ + 'name' : 'disjoint-group-new-data', + 'infname' : self.datafname, + 'parameter_dir' : self.paramdir('new' if args.bust_cache else 'ref', 'data'), + 'is_simu' : False, + }) + + for tcfg in test_configs: + disjoint_dir = '%s/%s' % (self.dirs('new'), tcfg['name']) + if os.path.exists(disjoint_dir): + shutil.rmtree(disjoint_dir) + + # step 1: disjoint-group + cmd = '%s disjoint-group --dont-write-git-info --disjoint-dir %s' % (self.partis_path, disjoint_dir) + if args.paired: + cmd += ' --paired-loci --paired-indir %s' % tcfg['paired_indir'] + else: + cmd += ' --infname %s --locus %s' % (tcfg['infname'], args.locus) + cmd += ' --parameter-dir %s' % tcfg['parameter_dir'] + if tcfg['is_simu']: + cmd += ' --is-simu' + cmd += ' %s' % ' '.join(self.common_extras) + logstr = '%s %s' % (utils.color('green', tcfg['name'] + ' (step 1: group)', width=40, padside='right'), cmd) + print(logstr if utils.len_excluding_colors(logstr) < args.print_width else logstr[:args.print_width] + '[...]') + logfile = open(self.logfname, 'a') + logfile.write(logstr + '\n') + logfile.close() + start = time.time() + try: + check_call(cmd + ' 1>>' + self.logfname + ' 2>>' + self.logfname, shell=True) + except CalledProcessError: + print(' log tail: %s' % self.logfname) + print(utils.pad_lines(check_output(['tail', self.logfname], universal_newlines=True))) + sys.exit(1) + + # step 2: partition each group + manifest = disjointgrouper.read_manifest('%s/manifest.yaml' % disjoint_dir) + for ginfo in manifest['groups']: + fasta_path = '%s/%s' % (disjoint_dir, ginfo['fasta_path']) + partition_path = '%s/groups/cdr3-%d/partition-%s.yaml' % (disjoint_dir, ginfo['cdr3_length'], ginfo['locus']) + pdir = '%s/%s' % (tcfg['parameter_dir'], ginfo['locus']) if args.paired else tcfg['parameter_dir'] + cmd = '%s partition --dont-write-git-info --infname %s --outfname %s --parameter-dir %s --locus %s' % (self.partis_path, fasta_path, partition_path, pdir, ginfo['locus']) + # do not pass --is-simu for per-group FASTAs (no simulation germline info embedded, same as bin/partis line 807) + cmd += ' %s' % ' '.join(self.common_extras) + logstr = '%s %s' % (utils.color('green', ' group %d (cdr3 %d, %s)' % (ginfo['group_id'], ginfo['cdr3_length'], ginfo['locus']), width=40, padside='right'), cmd) + print(logstr if utils.len_excluding_colors(logstr) < args.print_width else logstr[:args.print_width] + '[...]') + logfile = open(self.logfname, 'a') + logfile.write(logstr + '\n') + logfile.close() + try: + check_call(cmd + ' 1>>' + self.logfname + ' 2>>' + self.logfname, shell=True) + except CalledProcessError: + print(' log tail: %s' % self.logfname) + print(utils.pad_lines(check_output(['tail', self.logfname], universal_newlines=True))) + sys.exit(1) + # update manifest with partition path + ginfo['partition_path'] = 'groups/cdr3-%d/partition-%s.yaml' % (ginfo['cdr3_length'], ginfo['locus']) + + # write updated manifest with partition paths + with open('%s/manifest.yaml' % disjoint_dir, 'w') as mfile: + yaml.dump(manifest, mfile, width=400, default_flow_style=False) + + # step 3: assemble-groups + cmd = '%s assemble-groups --dont-write-git-info --disjoint-dir %s' % (self.partis_path, disjoint_dir) + cmd += ' %s' % ' '.join(self.common_extras) + logstr = '%s %s' % (utils.color('green', tcfg['name'] + ' (step 3: assemble)', width=40, padside='right'), cmd) + print(logstr if utils.len_excluding_colors(logstr) < args.print_width else logstr[:args.print_width] + '[...]') + logfile = open(self.logfname, 'a') + logfile.write(logstr + '\n') + logfile.close() + try: + check_call(cmd + ' 1>>' + self.logfname + ' 2>>' + self.logfname, shell=True) + except CalledProcessError: + print(' log tail: %s' % self.logfname) + print(utils.pad_lines(check_output(['tail', self.logfname], universal_newlines=True))) + sys.exit(1) + + # step 4 (simu only): validate disjointness against ground truth + if tcfg['is_simu']: + print(' validating disjointness against ground truth...') + loci = utils.sub_loci('ig') if args.paired else [args.locus] + simu_dir = tcfg.get('paired_indir', None) + simu_fname = tcfg.get('infname', None) + n_split = 0 + for ltmp in loci: + if simu_dir is not None: + sfname = '%s/%s.yaml' % (simu_dir, ltmp) + else: + sfname = simu_fname + sglfo, salist, _ = utils.read_yaml_output(sfname, dont_add_implicit_info=True) + family_cdr3s = collections.defaultdict(set) + for line in salist: + family_cdr3s[line['reco_id']].add(line['cdr3_length']) + split_families = {r: c for r, c in family_cdr3s.items() if len(c) > 1} + n_split += len(split_families) + if len(split_families) > 0: + print(' %s %s: %d families split across CDR3 length groups:' % (utils.color('red', 'error'), ltmp, len(split_families))) + for rid, c3s in split_families.items(): + print(' %s: cdr3 lengths %s' % (rid, sorted(c3s))) + else: + print(' %s: %d families, all have uniform CDR3 length' % (ltmp, len(family_cdr3s))) + if n_split > 0: + raise Exception('disjointness validation failed: %d families split across CDR3 length groups' % n_split) + + elapsed = time.time() - start + self.run_times[tcfg['name']] = elapsed + print(' %s' % utils.color('green', 'ok (%.1fs)' % elapsed)) + # ---------------------------------------------------------------------------------------- def test(self, args): if not args.dont_run: self.run(args) + if not args.quick: + self.run_disjoint_group_tests(args) if args.dry_run or args.bust_cache or args.quick: return self.compare_production_results(['cache-parameters-simu'])