==========
summary.py
==========

.. code-block:: bash

	usage: summary.py

	Summarize Autometa results writing genome fastas and their respective
	taxonomies/assembly metrics for respective metagenomes

	optional arguments:
	  -h, --help            show this help message and exit
	  --binning-main filepath
	                        Path to Autometa binning main table (output from
	                        --binning-main argument) (default: None)
	  --markers filepath    Path to annotated markers respective to domain
	                        (bacteria or archaea) binned (default: None)
	  --metagenome filepath
	                        Path to metagenome assembly (default: None)
	  --dbdir dirpath       Path to user taxonomy database directory (Required for
	                        retrieving metabin taxonomies) (default: None)
	  --dbtype {ncbi,gtdb}  Taxonomy database type to use (NOTE: must correspond
	                        to the same database type used during contig taxon
	                        assignment.) (default: ncbi)
	  --binning-column str  Binning column to use for grouping metabins (default:
	                        cluster)
	  --output-stats filepath
	                        Path to write metabins stats table (default: None)
	  --output-taxonomy filepath
	                        Path to write metabins taxonomies table (default:
	                        None)
	  --output-metabins dirpath
	                        Path to output directory. (Directory must not exist.
	                        This directory will be created.) (default: None)