lca.py
usage: lca.py
Script to determine Lowest Common Ancestor
optional arguments:
-h, --help show this help message and exit
--blast filepath Path to BLAST results table respective to `orfs`.
(Note: The table provided must be in outfmt=6)
(default: None)
--dbdir dirpath Path to taxonomy databases directory. (default:
NCBI_DIR)
--dbtype {ncbi,gtdb} Taxonomy database to use (default: ncbi)
--lca-output filepath
Path to write LCA results. (default: None)
--sseqid2taxid-output filepath
Path to write qseqids sseqids to taxids translations
table (default: None)
--lca-error-taxids filepath
Path to write table of blast table qseqids that were
assigned root due to a missing taxid (default: None)
--verbose Add verbosity to logging stream. (default: False)
--force Force overwrite if results already exist. (default:
False)
--cache dirpath Path to cache pickled LCA database objects. (default:
None)
--only-prepare-cache Only prepare the LCA database objects and write to
provided --cache parameter (default: False)
--force-cache-overwrite
Force overwrite if results already exist. (default:
False)