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geNomad v1.1.0
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@apcamargo apcamargo released this 23 Aug 00:03
· 133 commits to main since this release
v1.1.0
95af5f5

Added

  • Dockerfile for version 1.0.0.
  • Sequence class: add support for str in __eq__.
  • Sequence class: add a __hash__ method.
  • Compute marker enrichment in the marker-classification module.
  • Add columns for plasmid and virus marker enrichment to the _plasmid_summary.tsv and _virus_summary.tsv files.
  • Set --min-plasmid-marker-enrichment and --min-virus-marker-enrichment to 0 as default. This will alter the results when using default parameters.
  • Add support for plasmid and virus hallmarks. Requires geNomad database v1.1.
  • Add CONJscan annotations to _plasmid_summary.tsv. Requires geNomad database v1.1.

Changed

  • Sequence class: simplify has_dtr return statement.
  • Sequence class: make __repr__ more friendly for long sequences.
  • Sequence class: rename the id property to accession.
  • Amino acids are now written to _provirus_aragorn.tsv.
  • Update the XGBoost model file to the .ubj format.
  • Require xgboost >=1.6.
  • The taxonomic lineage in _taxonomy.tsv and _virus_summary.tsv will use Viruses as the highest rank, instead of root.
  • Change order of the columns in _plasmid_summary.tsv and _virus_summary.tsv.
  • Explicitly set fraction to 0.5 in taxopy.find_majority_vote.

Fixed

  • tRNA coordinates are now 1-indexed.
  • Write summary_execution_info.
  • Fix a problem in DatabaseDownloader.get_version where only the major version was compared.
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