======
lca.py
======

.. code-block:: bash

	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)