---
name: "fastaq_search_for_seq"
section: "1"
platform: "linux"
package: "fastaq"
version: "1.5.0-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastaq_search_for_seq"
---

# fastaq\_search\_for\_seq(1)

## 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 (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.