===================
recursive_dbscan.py
===================

.. code-block:: bash

	usage: recursive_dbscan.py

	Perform marker gene guided binning of metagenome contigs using annotations
	(when available) of sequence composition, coverage and homology.

	optional arguments:
	  -h, --help            show this help message and exit
	  --kmers filepath      Path to embedded k-mers table (default: None)
	  --coverages filepath  Path to metagenome coverages table (default: None)
	  --gc-content filepath
	                        Path to metagenome GC contents table (default: None)
	  --markers filepath    Path to Autometa annotated markers table (default:
	                        None)
	  --output-binning filepath
	                        Path to write Autometa binning results (default: None)
	  --output-main filepath
	                        Path to write Autometa main table used during/after
	                        binning (default: None)
	  --clustering-method {dbscan,hdbscan}
	                        Clustering algorithm to use for recursive binning.
	                        (default: dbscan)
	  --completeness 0 < float <= 100
	                        completeness cutoff to retain cluster. e.g. cluster
	                        completeness >= `completeness` (default: 20.0)
	  --purity 0 < float <= 100
	                        purity cutoff to retain cluster. e.g. cluster purity
	                        >= `purity` (default: 95.0)
	  --cov-stddev-limit float
	                        coverage standard deviation limit to retain cluster
	                        e.g. cluster coverage standard deviation <= `cov-
	                        stddev-limit` (default: 25.0)
	  --gc-stddev-limit float
	                        GC content standard deviation limit to retain cluster
	                        e.g. cluster GC content standard deviation <= `gc-
	                        content-stddev-limit` (default: 5.0)
	  --taxonomy filepath   Path to Autometa assigned taxonomies table (default:
	                        None)
	  --starting-rank {superkingdom,phylum,class,order,family,genus,species}
	                        Canonical rank at which to begin subsetting taxonomy
	                        (default: superkingdom)
	  --reverse-ranks       Reverse order at which to split taxonomy by canonical-
	                        rank. When `--reverse-ranks` is given, contigs will be
	                        split in order of species, genus, family, order,
	                        class, phylum, superkingdom. (default: False)
	  --rank-filter {superkingdom,phylum,class,order,family,genus,species}
	                        Taxonomy column canonical rank to subset by provided
	                        value of `--rank-name-filter` (default: superkingdom)
	  --rank-name-filter RANK_NAME_FILTER
	                        Only retrieve contigs with this name corresponding to
	                        `--rank-filter` column (default: bacteria)
	  --verbose             log debug information (default: False)
	  --cpus int            Number of cores to use by clustering method (default
	                        will try to use as many as are available) (default:
	                        -1)