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GFFtools-GX

A collection of tools for converting genome annotation between GTF, BED, GenBank and GFF.

INTRODUCTION

Several genome annotation centers provide their data in GTF, BED, GFF and GenBank format. I have few programs, they mainly deals with converting between GTF, BED GenBank and GFF formats. They are extensively tested with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. These programs can be easily integrated into your galaxy instance.

CONTENTS

Included utilities are:

BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF
GBK-to-GFF: convert data from genbank format to GFF
GFF-to-BED: convert data from GFF to 12 column BED format
GFF-to-GTF: convert data from GFF to GTF 
GTF-to-GFF: convert data from GTF to valid GFF

test-data: 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: 

exmaple: 
sh run_functional_tests.sh -id fml_gtf2gff
REQUIREMENTS
python2.6 or 2.7 and biopython  

Galaxy should be able to automatically install biopython via Galaxy toolshed.
COMMENTS/QUESTIONS

I can be reached at vipin [at] cbio.mskcc.org

LICENSE

Copyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society

          2013-2015, Memorial Sloan Kettering Cancer Center
          Vipin T Sreedharan <vipin@cbio.mskcc.org>  

All rights reserved.

Licensed under the BSD 2-Clause License: http://opensource.org/licenses/BSD-2-Clause

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:

    * Redistributions of source code must retain the above copyright notice,
      this list of conditions and the following disclaimer.

    * Redistributions in binary form must reproduce the above copyright notice,
      this list of conditions and the following disclaimer in the documentation
      and/or other materials provided with the distribution.

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COURTESY

To the Galaxy Team.

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