markers.py
usage: markers.py
Annotate ORFs with kingdom-specific marker information
optional arguments:
-h, --help show this help message and exit
--orfs ORFS Path to a fasta file containing amino acid sequences
of open reading frames (default: None)
--kingdom {bacteria,archaea}
kingdom to search for markers (default: bacteria)
--hmmscan HMMSCAN Path to hmmscan output table containing the respective
`kingdom` single-copy marker annotations. (default:
None)
--out OUT Path to write filtered annotated markers corresponding
to `kingdom`. (default: None)
--dbdir DBDIR Path to directory containing the single-copy marker
HMM databases. (default: MARKERS_DIR)
--hmmdb HMMDB Path to single-copy marker HMM databases. (default:
None)
--cutoffs CUTOFFS Path to single-copy marker cutoff tsv. (default: None)
--force Whether to overwrite existing provided annotations.
(default: False)
--parallel Whether to use hmmscan parallel option. (default:
False)
--gnu-parallel Whether to run hmmscan using GNU parallel. (default:
False)
--cpus CPUS Number of cores to use for parallel execution.
(default: 8)
--seed SEED Seed to set random state for hmmscan. (default: 42)