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v0.6.0

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@jamesck2 jamesck2 released this 28 Oct 19:22
· 21 commits to main since this release
v0.6.0
1fdeae7

0.6.0

  • lgbm_model.joblib, lgbm_feature_names.joblib, lgbm_thresholds.joblib:

    • Improvements to the viral origin confidence LGBM
    • Added additional features that consider the V/VL-scores of the 3 nearest genes on the left and right flanks of each gene, and the V/VL-scores of the nearest mobile genes

  • AMGs.tsv, APGs.tsv, AReGs.tsv, FOAM.tsv, hmm_id_to_name.csv, mobile_genes.csv, viral_hallmark_genes.csv:

    • Slight modifications to the AMG, APG, AReG, viral hallmark, and mobile genes lists
    • Updated the all-HMM list with updated dbCAN and missing FOAM annotations

  • download_db.py:

    • Added functionality to download and prepare the database-provided bitscore thresholds for KEGG and FOAM using the same versions as the downloaded HMMs
    • Fixed incorrect version label for the dbCAN HMM files

  • CheckAMG_annotate.smk:

    • Updated the KEGG and FOAM threshold file locations from the 'files' directory (with the AMG, APG, AReG, etc. tables) to the 'db' directory (with the HMM profiles)
    • Now puts the snakemake *.done files in their own folder

  • CheckAMG_annotate.py:

    • Set up a subfolder for snakemake files

  • main.py:

    • Changed the default --scaling_factor from 1.6 to 1.8 due to KEGG threshold updates

  • pyproject.toml:

    • Added a missing scikit-learn dependency
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