fastaq_search_for_seq (1)

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

fastaq_search_for_seq was originally written by Martin Hunt ([email protected])

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.