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)