v1.3.2: The following conda dependencies were upgraded: hmmer =3.4,...
v1.3.2: The following conda dependencies were upgraded: hmmer =3.4, snakemake-minimal >=8.4, biopython =1.83 and blast =2.15 ; The bcbio-gff dependency is not compatible with the latest version of biopython and snakemake-minimal and has been removed. The generation of GFF files (_icescreen.gff and _source.gff) is now handled by a specific module in ICEscreen ; Bug fixe [Issue #17](https://forgemia.inra.fr/ices_imes_analysis/icescreen/-/issues/17) _icescreen.gff files (visualization folder) had multiple issues: The phase for the CDS was incorrect, there were only 8 tab-separated fields instead of 9, truncated gene location were not reported.
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- .gitignore 1 addition, 0 deletions.gitignore
- .gitlab-ci.yml 2 additions, 2 deletions.gitlab-ci.yml
- LOG_public_releases.md 9 additions, 8 deletionsLOG_public_releases.md
- icescreen 17 additions, 16 deletionsicescreen
- icescreen_detection_ME/src/rulesAddIntegrases.py 2 additions, 2 deletionsicescreen_detection_ME/src/rulesAddIntegrases.py
- icescreen_detection_SP/src/process_blastp_results.py 8 additions, 4 deletionsicescreen_detection_SP/src/process_blastp_results.py
- icescreen_detection_SP/src/process_hmmscan_fp.py 1 addition, 1 deletionicescreen_detection_SP/src/process_hmmscan_fp.py
- icescreen_detection_SP/src/process_hmmscan_results.py 2 additions, 2 deletionsicescreen_detection_SP/src/process_hmmscan_results.py
- icescreen_detection_SP/src/reannot_SP.py 1 addition, 0 deletionsicescreen_detection_SP/src/reannot_SP.py
- icescreen_envs/icescreen_env_1-3-2.yml 6 additions, 6 deletionsicescreen_envs/icescreen_env_1-3-2.yml
- icescreen_formatting/GFF3_Module.py 163 additions, 0 deletionsicescreen_formatting/GFF3_Module.py
- icescreen_formatting/genbank_to_gff3_and_fasta.py 8 additions, 3 deletionsicescreen_formatting/genbank_to_gff3_and_fasta.py
- icescreen_formatting/generate_annotation_files.py 23 additions, 97 deletionsicescreen_formatting/generate_annotation_files.py
- icescreen_pipelines/icescreen.snakefile 1 addition, 1 deletionicescreen_pipelines/icescreen.snakefile
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