A collection of tools for converting genome annotation between GTF (Gene Transfer Format), BED (Browser Extensible Data) and GFF (Generic Feature Format)

INTRODUCTION

Several genome annotation centers provide their data in GTF, BED, GFF3 etc. I have few programs 
they mainly deals with converting between GTF, BED and GFF3 formats. They are extensively tested 
with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. Please follow the 
instructions below to clone these tools into your galaxy instance.

CONTENTS

galaxy: Contains tool configuration files in *.xml format. 

    Tool configuration files. Please add right path to locate the scripts.

    gtf_to_gff3.xml

    gff3_to_gtf.xml

    bed_to_gff3.xml

    gff3_to_bed.xml

t: Test data set. (move to your galaxy root folder/test-data/)
    
    You may need to move the test files into your test-data directory so galaxy can find them. 
    If you want to run the functional tests eg as: 

    sh run_functional_tests.sh -id fml_gtf2gff3

scripts: Python based and Perl based scripts. 

    gtf_to_gff3_converter.py: This tool converts data from GTF format to valid GFF3 format.
    
    gff3_to_gtf_converter.pl: This tool converts data from GFF3 format to GTF format.

    bed_to_gff3_converter.py: This tool converts data from a 12 column UCSC wiggle BED format to GFF3 format.

    gff3_to_bed_converter.py: This tool converts gene transcript annotation from GFF3 format to UCSC wiggle 12 column BED format.

REQUIREMENTS

    Python, Perl and if you are interested to use gff3_to_gtf_converter.pl please install Bio::Perl module.

COMMENTS/QUESTIONS 

I can be reached at vipin.ts@tuebingen.mpg.de

LICENSE

Copyright (C) 2010 Friedrich Miescher Laboratory of the Max Planck Society

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.

COURTESY

To the Galaxy Team.