NAME
fastaq_search_for_seq
DESCRIPTION
fastaq_search_for_seq [options] <fasta/q in> <outfile> <search_string>
Searches for an exact match on a given string and its reverese complement, in every sequences of a fasta/q file. Case insensitive. Guaranteed to find all hits
positional arguments:
- infile
-
Name of input fasta/q file
- outfile
-
Name of outputfile. Tab-delimited output: sequence name, position, strand
- search_string
-
String to search for in the sequences
optional arguments:
- -h, --help
-
show this help message and exit
AUTHOR
fastaq_search_for_seq 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.