Update stable to v1.0.4

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.3
+current_version = 1.0.4
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[a-z0-9+]+)

.github/workflows/build.yaml

@@ -73,35 +73,35 @@ jobs:
             --token "${{ secrets.ANACONDA_TOKEN }}" \
             conda/bactabolize/
 
-  build_and_publish_on_dockerhub:
-    runs-on: ubuntu-latest
-    needs:
-      - get_version
-      - build_and_publish_on_conda
-    # Only push on push to stable, which implicitly should be only version bumps
-    if: github.ref == 'refs/heads/stable'
-    defaults:
-      run:
-        shell: bash -l {0}
-    env:
-      DOCKERHUB_REPO: "docker.io/scwatts/bactabolize"
-      VERSION: ${{ needs.get_version.outputs.version }}
-    steps:
-      - name: Checkout code
-        id: git_checkout
-        uses: actions/checkout@v3
-      - name: Build Docker image
-        run: |
-          docker build \
-            --tag "${DOCKERHUB_REPO}:${VERSION}" \
-            --file docker/Dockerfile \
-            ./
-      - name: DockerHub auth
-        run: |
-          echo "${{ secrets.DOCKERHUB_TOKEN }}" | \
-            docker login \
-              --username "${{ secrets.DOCKERHUB_USERNAME }}" \
-              --password-stdin
-      - name: DockerHub push
-        run: |
-          docker push "${DOCKERHUB_REPO}:${VERSION}"
+  # build_and_publish_on_dockerhub:
+  #   runs-on: ubuntu-latest
+  #   needs:
+  #     - get_version
+  #     - build_and_publish_on_conda
+  #   # Only push on push to stable, which implicitly should be only version bumps
+  #   if: github.ref == 'refs/heads/stable'
+  #   defaults:
+  #     run:
+  #       shell: bash -l {0}
+  #   env:
+  #     DOCKERHUB_REPO: "docker.io/scwatts/bactabolize"
+  #     VERSION: ${{ needs.get_version.outputs.version }}
+  #   steps:
+  #     - name: Checkout code
+  #       id: git_checkout
+  #       uses: actions/checkout@v3
+  #     - name: Build Docker image
+  #       run: |
+  #         docker build \
+  #           --tag "${DOCKERHUB_REPO}:${VERSION}" \
+  #           --file docker/Dockerfile \
+  #           ./
+  #     - name: DockerHub auth
+  #       run: |
+  #         echo "${{ secrets.DOCKERHUB_TOKEN }}" | \
+  #           docker login \
+  #             --username "${{ secrets.DOCKERHUB_USERNAME }}" \
+  #             --password-stdin
+  #     - name: DockerHub push
+  #       run: |
+  #         docker push "${DOCKERHUB_REPO}:${VERSION}"

bactabolize/__init__.py

@@ -1,2 +1,2 @@
 __program_name__ = 'bactabolize'
-__version__ = '1.0.3'
+__version__ = '1.0.4'

bactabolize/annotate.py

@@ -126,12 +126,22 @@ def match_existing_orfs_updated_annotations(new_fp, existing_fp, overlap_min=0.8
         # Find overlaps
         positions = contig_positions_new[contig] + contig_positions_existing[contig]
         features_matched = discover_overlaps(positions, overlap_min)
-        # Discover those not matched
-        features_matched_flat = set()
-        for features in features_matched:
-            features_matched_flat.update(features)
-        new_unmatched = set(features_new[contig]).difference(features_matched_flat)
-        existing_unmatched = set(features_existing[contig]).difference(features_matched_flat)
+
+        # Discover those not matched using location comparison
+        features_matched_new = [f[0] for f in features_matched]
+        features_matched_existing = [f[1] for f in features_matched]
+
+        # Find unmatched features by comparing locations
+        new_unmatched = []
+        for feature in features_new[contig]:
+            if not any(f.location == feature.location for f in features_matched_new):
+                new_unmatched.append(feature)
+
+        existing_unmatched = []
+        for feature in features_existing[contig]:
+            if not any(f.location == feature.location for f in features_matched_existing):
+                existing_unmatched.append(feature)
+
         # For each matched update bounds update locus tag, product, gene (if present) to match existing
         quals = ('locus_tag', 'product', 'gene')
         features_updated = list()
@@ -141,6 +151,7 @@ def match_existing_orfs_updated_annotations(new_fp, existing_fp, overlap_min=0.8
                     continue
                 feature_new.qualifiers[qual] = feature_existing.qualifiers[qual]
             features_updated.append(feature_new)
+
         # Add existing ORFs that had no match
         features_updated.extend(new_unmatched)
         features_updated.extend(existing_unmatched)
@@ -152,6 +163,7 @@ def match_existing_orfs_updated_annotations(new_fp, existing_fp, overlap_min=0.8
         print(f'\t{len(existing_unmatched)} existing features unmatched')
         print(f'\t{len(new_unmatched)} re-annotated features unmatched')
         print(f'\t{len(features_updated)} total features')
+
     # Update new genbank with new feature set
     update_genbank_annotations(new_fp, contig_features_updated)
 
@@ -179,7 +191,8 @@ def discover_overlaps(positions, overlap_min):
     # pylint: disable=too-many-branches
     in_new = list()
     in_existing = list()
-    features_matched = set()
+    # Change from set to list to store matches
+    features_matched = []
     for position in sorted(positions, key=lambda k: k['position']):
         # Add features we're entering and remove those we're exiting
         if position['type'] == 'start':
@@ -199,7 +212,12 @@ def discover_overlaps(positions, overlap_min):
             for feature_existing in in_existing:
                 if feature_new.strand != feature_existing.strand:
                     continue
-                if (feature_new, feature_existing) in features_matched:
+                # Check if this pair is already matched by comparing locations
+                already_matched = any(
+                    fn.location == feature_new.location and fe.location == feature_existing.location 
+                    for fn, fe in features_matched
+                )
+                if already_matched:
                     continue
                 # Get overlap
                 start = max(feature_new.location.start, feature_existing.location.start)
@@ -212,7 +230,7 @@ def discover_overlaps(positions, overlap_min):
                     # Update note to include overlap information
                     [note_new] = feature_new.qualifiers['note']
                     feature_new.qualifiers['note'][0] = f'{note_new};overlap:{overlap_new:.2f}'
-                    features_matched.add((feature_new, feature_existing))
+                    features_matched.append((feature_new, feature_existing))
     return features_matched
 
 

conda/bactabolize/meta.yaml

@@ -17,6 +17,13 @@ requirements:
   run:
     - python ==3.9
     - biopython ==1.79
+    - glpk ==5.0
+    - swiglpk ==5.0.10
+    - urllib3 ==2.2.2
+    - cchardet ==2.1.7
+    - tabulator ==1.25.1
+    - goodtables ==2.5.4
+    - openpyxl ==2.4.11
     - blast ==2.12.0
     - cobra ==0.21.0
     - prodigal ==2.6.3
@@ -28,7 +35,6 @@ requirements:
     - cookiecutter
     - depinfo ==1.7.0
     - gitpython
-    - goodtables ~=2.0
     - importlib_resources ==5.12.0
     - jinja2
     - numpydoc

data/media_definitions/tsa_sheep_blood_media.json

@@ -1,6 +1,6 @@
 {
   "name": "TSA_sheep_blood",
-  "exchanges":
+  "exchanges": {
     "EX_14glucan_e":  -1000,
     "EX_1Dgali_e":    -1000,
     "EX_ala__L_e":    -1000,

docker/Dockerfile

@@ -2,7 +2,7 @@ FROM mambaorg/micromamba:0.24.0
 
 RUN \
   micromamba install -y -n base -c scwatts -c bioconda -c conda-forge -c defaults \
-    'bactabolize==1.0.3' && \
+    'bactabolize==1.0.4' && \
   micromamba clean --all --yes
 
 ENV PATH="/opt/conda/bin:/opt/conda/condabin:${PATH}"

requirements-dev.yaml

@@ -16,6 +16,13 @@ dependencies:
   - pylint >=2.5,<=2.14  # NOTE(SW): upper bound on version to avoid installing broken package
   # Dependencies
   - biopython ==1.79
+  - glpk ==5.0
+  - swiglpk ==5.0.10
+  - urllib3 ==2.2.2
+  - cchardet ==2.1.7
+  - tabulator ==1.25.1
+  - goodtables ==2.5.4
+  - openpyxl ==2.4.11
   - blast ==2.12.0
   - cobra ==0.21.0
   - prodigal ==2.6.3

setup.py

@@ -11,7 +11,7 @@
     description='Bactabolize python package',
     author='Stephen Watts',
     license='GPLv3',
-    url='https://github.com/scwatts/bactabolize',
+    url='https://github.com/kelwyres/bactabolize',
     test_suite='tests',
     packages=setuptools.find_packages(),
     package_data={'bactabolize': ['data/**']},