NAME¶

fastaq_filter

DESCRIPTION¶

fastaq_filter [options] <infile> <outfile> Filters a fasta/q file by sequence length and/or by name matching a regular expression

positional arguments:¶

infile

Name of fasta/q file to be filtered

outfile

Name of output fasta/q file

optional arguments:¶

-h, --help

show this help message and exit

--min_length INT

Minimum length of sequence to keep [0]

--max_length INT

Maximum length of sequence to keep [inf]

--regex REGEX

If given, only reads with a name matching the regular expression will be kept

--ids_file IDS_FILE

If given, only reads whose ID is in th given file will be used. One ID per line of file.

-v, --invert

Keep sequences that do not match the filters

AUTHOR¶

fastaq_filter was originally written by Martin Hunt (mh12@sanger.ac.uk)

COPYING¶

Wellcome Trust Sanger Institute Copyright © 2013 Wellcome Trust Sanger Institute This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.