==========
hmmscan.py
==========

.. code-block:: bash

	usage: hmmscan.py

	Retrieves markers with provided input assembly

	positional arguments:
	  orfs            </path/to/assembly.orfs.faa>
	  hmmdb           </path/to/hmmpressed/hmmdb>
	  cutoffs         </path/to/hmm/cutoffs.tsv>
	  hmmscan         </path/to/hmmscan.tblout>
	  markers         </path/to/markers.tsv>

	optional arguments:
	  -h, --help      show this help message and exit
	  --force         force overwrite of out filepath
	  --cpus CPUS     num cpus to use
	  --parallel      enable hmmer multithreaded parallelization
	  --gnu-parallel  enable GNU parallelization