fastaq_filter1
Overview
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
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.