Mercurial > repos > vipints > fml_gff3togtf
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author | devteam |
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date | Tue, 04 Nov 2014 12:15:19 -0500 (2014-11-04) |
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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 Tool configuration files in *.xml format. gtf_to_gff.xml gff_to_gtf.xml bed_to_gff.xml gff_to_bed.xml gbk_to_gff.xml gff_fmap.xml Python based scripts. gtf_to_gff.py: convert data from GTF to valid GFF3. gff_to_gtf.py: convert data from GFF3 to GTF. bed_to_gff.py: convert data from a 12 column UCSC wiggle BED format to GFF3. gff_to_bed.py: convert gene transcript annotation from GFF3 to UCSC wiggle 12 column BED format. gbk_to_gff.py: convert data from genbank format to GFF. gff_fmap.py: find the relation between different features described in a GFF file. GFFParser.py: Parse GFF/GTF files. helper.py: Utility functions. 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 python 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 2013-2014 Memorial Sloan Kettering Cancer Center 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.