Description

Relabel tree and msa based on input label dictionaries

Epilog

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

Usage:

usage: metatag relabel [-h] [args] 

Arguments

short	long	default	help
-h	--help		show this help message and exit
	--tree	None	path to tree in newick format
	--labels	None	path to label dict in pickle format. More than one space-separated path can be input
	--label_prefixes	None	prefix(es) to be added to sequences in each label dict,input in same order as labels.More than one space-separated prefix can be input
	--taxonomy		assign GTDB taxonomy to labels containing MMP identifiers
	--aln	None	path to fasta alignment file to be relabelled
	--outdir	None	path to output directory
	--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.