Add a new command to metagenomics.py called taxlevel_plurality (inspired by taxlevel_summary) that takes a kraken (or kraken2 or krakenuniq) summary report as input and reports on the top taxa identified under a focal taxon of interest (e.g. "Viruses"). This emits a tabular file ranked in descending order of the taxa with the highest read counts (not including children).
Add new command to metagenomics.py called filter_taxids_to_focal_hits to reduce a list of taxids to those related to outputs from taxlevel_plurality.
Also a few other unrelated bits included in this PR:
build updates: remove scheduled builds from GHActions (they don't like it and auto-disable builds if we don't touch the codebase much), add merge_group functionality, bump some versions of GHActions builders that are deprecated
update viral-core 2.2.3 to 2.2.4
clean up a bunch of stray top level python methods in metagenomics.py and move into the TaxonomyDb class for proper hygiene
Add a new command to
metagenomics.pycalledtaxlevel_plurality(inspired bytaxlevel_summary) that takes a kraken (or kraken2 or krakenuniq) summary report as input and reports on the top taxa identified under a focal taxon of interest (e.g. "Viruses"). This emits a tabular file ranked in descending order of the taxa with the highest read counts (not including children).Add new command to
metagenomics.pycalledfilter_taxids_to_focal_hitsto reduce a list of taxids to those related to outputs from taxlevel_plurality.Also a few other unrelated bits included in this PR: