Description

Database preprocessing: removal of duplicated sequences and of sequences with illegal symbols. To preferentially keep one duplicate sequence over another, place preferred sequences first.

Epilog

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

Usage:

usage: metatag preprocess [-h] [args] 

Arguments

short	long	default	help
-h	--help		show this help message and exit
	--in	None	path to fasta file or directory containing fasta files
	--dna		declare if sequences are nucleotides. Defaults to peptide sequences.
	--translate		choose whether nucleotide sequences are translated with prodigal
	--export-duplicates		choose whether duplicated sequences are exported to file (same directory than outfile)
	--outfile	None	path to output fasta file
	--relabel		relabel record IDs with numeral ids
	--relabel_prefix	None	prefix to be added to sequence IDs