revcom_seq

revcom_seq

revcom_seq.pl is a script to reverse complement (multi-)sequence files.

• Synopsis
• Description
• Usage
• Options
• Output
• Run environment
• Dependencies
• Author - contact
• Citation, installation, and license
• Changelog

Synopsis

perl revcom_seq.pl seq-file.embl > seq-file_revcom.embl

or

perl cat_seq.pl multi-seq_file.embl | perl revcom_seq.pl -i embl > seq_file_cat_revcom.embl

Description

This script reverse complements (multi-)sequence files. The features/annotations in RichSeq files (e.g. EMBL or GENBANK format) will also be adapted accordingly. Use option -o to specify a different output sequence format. Input files can be given directly via STDIN or as a file. If STDIN is used, the input sequence file format has to be given with option -i. Be careful to set the correct input format.

Usage

perl revcom_seq.pl -o gbk seq-file.embl > seq-file_revcom.gbk

or reverse complement all sequence files in the current working directory:

for file in *.embl; do perl revcom_seq.pl -o fasta "$file" > "${file%.embl}"_revcom.fasta; done

Options

• -h, -help

  Help (perldoc POD)

• -o=str, -outformat=str

  Specify different sequence format for the output [fasta, embl, or gbk]

• -i=str, -informat=str

  Specify the input sequence file format, only needed for STDIN input

• -v, -version

  Print version number to STDOUT

Output

• STDOUT

  The reverse complemented sequence file is printed to STDOUT. Redirect or pipe into another tool as needed.

Run environment

The Perl script runs under Windows and UNIX flavors.

Dependencies

• BioPerl (tested version 1.007001)

Author - contact

Andreas Leimbach (aleimba[at]gmx[dot]de; Microbial Genome Plasticity, Institute of Hygiene, University of Muenster)

Citation, installation, and license

For citation, installation, and license information please see the repository main README.md.

Changelog

• v0.2 (2015-12-10)
  • included a POD instead of a simple usage text
  • included pod2usage with Pod::Usage
  • included 'use autodie' pragma
  • options with Getopt::Long
  • output format now specified with option -o
  • included version switch, -v
  • allowed file and STDIN input, instead of only file; thus new option -i for input format
  • output printed to STDOUT now, instead of output file
  • fixed bug, that only first sequence in multi-sequence file is reverse complemented. Now all sequences in a multi-seq file are reverse complemented.
• v0.1 (2013-02-08)