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 ([email protected])
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.