Description

Build peptide reference database

Epilog

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

Usage:

usage: metatag database [-h] [args] 

Arguments

short	long	default	help
-h	--help		show this help message and exit
	--hmms	None	a single or a list of space-separated paths to tigrfam or pfam models
	--in	None	path to peptide database
	--outdir	None	path to output directory
	--prefix	``	prefix to be added to output files
	--relabel_prefixes	None	List of space-separated prefixes to be added to each hmm-derived set of sequences after relabelling. Only used if "--relabel" is set. Label prefixes set to "None" are assigned "ref_" by default.
	--max_sizes	None	maximum size of representative set of sequences for each hmm model. Each (space-separated) integer corresponds to a hmm model inputed in "--hmms", thus, sorted in the same order. A value of "None" may be given to a hmm model in the list, in which case the maximum number of sequences is unlimited for that hmm.Defaults to full set of sequences for all hmm modells inputed.
	--min_seq_length	None	minimum sequence length in reference database. Defaults to zero
	--max_seq_length	None	maximum sequence length in reference database. Defaults to inf
	--relabel		relabel record IDs with numerical ids. Unrequired to build database, but highly recommended to avoid possible conflicts downstream the pipeline.
	--nocdhit		do not run cd-hit on peptide database
	--remove_duplicates		remove duplicated sequences from final (merged) database
	--hmmsearch_args	None	a string of comma-separated additional arguments for each hmm passed to hmmsearch. e.g. inputing 3 hmms: " --cut_ga --cpu 4, --cut_nc, None". IMPORTANT: the string must be preceded by a white space. A single string may be provided, in which case the same additinal arguments will be passed for each hmm. Defaults to additional arguments string: "--cut_nc". If no additional arguments are needed, provide the value "None"