funannotate v1.7.3

• bug fix release. This will be the last release before updating the code for py3
• bug fix for remote #379
• improve GFF3 parsing in funannotate annotate allow for non-funannotate identifiers (hopefully this catches most of them)
• --aligners option was missing from help menu in train/update
• add --debug flag to funannotate iprscan -- there is potentially still an issue here combining results from the newest release of Interproscan -- I need some intermediate results to see what the problem is
• fix GO annotations parsing for more versions of goatools #363
• fix for bug in the "gene start or end in a gap" function
• make sure funannotate annotate re-runs tbl file generation if script is re-run
• fix in PASA function logic where PASA db not found if using --gff and --fasta input.

funannotate v1.7.2

• busco internal run now uses the local augustus config path, so hopefully write access to $AUGUSTUS_CONFIG_PATH is no longer required
• long reads are now processed to remove forward slashes from names if present -- this was causing problems with PASA #326 #250
• added augustus hints file generation when using RNA-seq data. Also added a check for --transcript_evidence if found in --transcript_alignments, ie so extra transcripts can be added instead of only those used to generate alignments in funannotate train. #360
• fix typo in funannotate check
• fix for proteinortho issue in funannotate compare #350

funannotate v1.7.1

A few updates to support bioconda integration -- namely either $TRINITYHOME or $TRINITY_HOME can be used. Also don't trust trinity packaged trimmomatic, use the conda version.

funannotate v1.7.0

Code has been repackaged to conform to a "proper" python package -- which means it now also resides on PyPi and a Bioconda package can be built. Along with the repackaging there are many improvements/fixes.

• funannotate now keeps track of "trained species" for all of the ab-initio gene predictors (Augustus, gene mark (optional), snap, GlimmerHMM, codingquarry). This requires all users to update their database, ie funannotate setup command. After running funannotate predict the software will output a JSON file containing the paths to the trained parameter files -- this can be used again for a different genome via the funannotate predict --parameters options. This parameter file can also be added to the database with the funannotate species -s genus_species -a parameters.json command. Running the funannotate species command will output a table in the command line of which species have training data. Addressed #320
• antiSMASH remote script fixed and parser updated for v5 output.
• added filtering for gene models that start/end in a gap that can sometimes show up after running funannotate update
• added a check for diamond version of the database and current copy -- this results in many hidden errors by users, ie diamond databases were created with an older/incompatible version than what is running currently.
• updated Augustus functional check
• removed RepeatModeler/RepeatMasker as strict dependencies. Due to RepBase change in usage license, repeatmasker/modeler are not available to most users. The funannotate mask command can still run this routine if you have the necessary dependencies installed, however, the current default is simply to run tantan masking. This is probably not sufficient for most genomes, thus happy to integrate a robust solution once one exists for repeat masking.
• augustus parameter training now done in the local output folder, so no longer need write access to $AUGUSTUS_CONFIG_PATH

funannotate v1.6.0

• support for antiSMASH v5.0 output #292 #299
• add snap and glimmerhmm request from #240. BUSCO is now run by default in funannotate predict if there is no PASA data -- BUSCO results used to train glimmerhmm and snap
• improved Phobius results parsing #259
• multi-threaded funannotate clean, thanks to @bogemad
• fix database links #300
• multi-threaded hisat2-build #303
• write all output files directly from tbl format -- fix bug associated with multi-transcript parsing from GenBank files
• bug fix for protein2genome exonerate mapping
• bug fixes for funannotate train and funannotate update
• added --min_coverage option to trinity workflow and set default to 5
• bug fixes for codingquarry predictions (RNA-seq only)
• improved error message for repeatmodeler/masker #298
• bug fix for remote searches
• bug fix for parsing input folders in annotate #302
• updated conda install docs --> which seems futile to keep this current....

funannotate v1.5.3

• updated the CAZYme dbCAN link
• fix string formatting in GeneMark-ET function

funannotate v1.5.2

• restructure augustus accessory scripts calls so that they don't have to be in same location as the exe, i.e. this used to be a bug if you used conda installed augustus as it puts the scripts in a different location than the default augustus release folder
• added a check to busco routine to default to a single thread if tblastn version is found that might have multithread issues
• allow a min number of gene models to use for Augustus training, --min_training_models in funannotate predict
• limit genemark to 64 cpus -- it will die if you try to give it more
• fix shortBAM declaration in funannotate update
• for genemark-ET set score of introns to 500, otherwise seems to be dying.
• updated weights for different gene models -- would be nice to have this be a customizable option....

funannotate v1.5.1

• updated dbCAN links
• important bug fix for RNA-seq analysis. the bam2gff3 function was not outputting the proper coordinates for crick stranded alignments for PASA, resulting valid minimap2 alignments being thrown out.
• several other minor bug fixes

funannotate v1.5.0

• add funannotate test as a unit test script to validate installation #212
• add CodingQuarry and StringTie integration into funannotate. Note these are "silent" dependencies, meaning if not installed this method will be skipped. If both tools are installed and RNA-seq data is used they will be run automatically #200
• fix contig number reporting in funannotate clean #210
• fix bug in a few of the accessory tools funannotate util
• update database to MiBIG v1.4

funannotate v1.4.2

• fix bug in train and update where script would die due to symlink error #189
• for predict the --protein_alignments option now takes GFF3 input (not exonerate output). This is to make consistent with the --transcript_alignments. Scripts now write hints file for augustus from the GFF3 file.
• similar to above, added funannotate util prot2genome which will run the diamond/exonerate mapping of proteins to the genome --> output is GFF3 file compatible with EVM. These data can then be passed to --protein_alignments