==========
markers.py
==========

.. code-block:: bash

	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)