seq_format-converter

seq_format-converter

A script to convert a sequence file to another format.

Synopsis

perl seq_format-converter.pl -i seq_file.gbk -f gbk -o embl

Description

This script converts a (multi-)sequence file of a specific format to a differently formatted output file. The most common sequence formats are: embl, fasta, and gbk (genbank).

Since sequence formats change from time to time, BioPerl is not always up to date. For all available BioPerl sequence formats see: http://www.bioperl.org/wiki/HOWTO:SeqIO#Formats. Warning: The bioperl-ext package and the io_lib library from the Staden package (http://staden.sourceforge.net/) need to be installed in order to read the scf, abi, alf, pln, exp, ctf, ztr formats.

Usage

perl seq_format-converter.pl -i seq_file -f in_format -o out_format

UNIX loop to reformat all sequence files in the current working directory

for i in *.[embl|gbk]; do perl seq_format-converter.pl -i $i -f [embl|gbk] -o [embl|fasta|gbk]; done

Options for seq_format-converter.pl

Mandatory options

• -i, -input

Input sequence file

• -f, -format

Input sequence format (e.g. 'embl' or 'gbk)

• -o, -out_format

Output sequence format (e.g. 'embl', 'fasta' or 'gbk)

Optional options

• -h, -help

Print usage

• -v, -version

Print version number

Output

• seq_file.[embl|fasta|gbk]

Output sequence file in the specified format

Run environment

The Perl script runs under Windows and UNIX flavors.

Dependencies (not in the core Perl modules)

• BioPerl (tested with version 1.006901)

Author/contact

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

Changelog

• v0.2 (03.02.2014)
  • allow short 'gbk' format instead of 'genbank'
  • also short 'gbk' file-extension for output file
  • included 'use autodie'
  • usage as HERE document
  • options with Getopt::Long
  • version switch
• v0.1 (10.11.2011)