Description

Assgin taxonomy and function to placed query sequences

Epilog

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

Usage:

usage: metatag assign [-h] [args] 

Arguments

short	long	default	help
-h	--help		show this help message and exit
	--jplace	None	path to placements jplace file
	--labels	None	path to label dict in pickle format. More than one space-separated path can be input
	--query_labels	None	path to query label dict in pickle format. More than one space-separated path can be input
	--ref_clusters	None	path to tsv file containing cluster assignment to each reference sequence id. Must contain one column named "id" and another (tab-separated) column named "cluster"
	--ref_cluster_scores	None	path to tsv file containing cluster quality scores assigned to each cluster in the reference tree. Contains one column named "cluster" and another (tab-separated) column named "score"
	--outgroup	None	path to text file containing IDs of sequences to be considered as an outgroup to root the tree. It can also be a fasta file from which sequence names will be extracted. It can also be a string containing a tag to filter record labels by it. The outgroup will be used to recover missing taxonomic infomation by gappa examine assign.
	--prefix	placed_tax_	prefix to be added to output files
	--outdir	None	path to output directory
	--max_placement_distance	None	Maximum allowed pendant distance to consider a placement as valid. Change distance measure with parameter: "distance_measure" (defaults to pendant length)
	--distance_measure	pendant	Choose distance measure to remove placements with distance larger than "max_placement_distance". Choose among: 1. "pendant": corresponding to pendant length of placement 2. "pendant_distal_ratio": ratio between pendant and distal distances 3. "pendant_diameter_ratio": ratio between pendant and tree diameter (largest pairwise distance) ratio. See https://github.com/lczech/gappa/wiki for a description of distal and pendant lengths.
	--min_placement_lwr	None	Minimum allowed placement LWR to consider a placement as valid. Values between 0 and 1.
	--duplicated_query_ids	None	path to text file containing duplicated query ids as output by seqkit rmdup
	--taxonomy_file	None	path to tsv containing taxonomy, formated like GTDB taxopaths, for each genome ID in reference database. Defaults to None, in which case a custom GTDB taxonomy database of marine prokaryotes is used.