Description

Count placed sequences based on taxon level, function and quality score

Epilog

Semidán Robaina Estévez (srobaina@ull.edu.es), 2021

Usage:

usage: metatag count [-h] [args] 

Arguments

short	long	default	help
-h	--help		show this help message and exit
	--taxtable	None	path to placements taxonomy table file
	--taxlevels	None	specify space-separated tax levels to count hits
	--cluster_ids	None	list of space-separated target cluster ids of the reference tree corresponding to the selected function to filter counts. If not provided, then all clusters in the tree are considered for counting.
	--score_threshold	None	cluster score threshold value to filter placement results
	--outdir	None	path to output directory
	--prefix	None	prefix to be added to output files
	--export_right_queries		export a tsv file containing queries with cluster assginments that passed provided filters (--score_threshold and/or --cluster_ids)