Mercurial > repos > vipints > fml_gff3togtf
comparison README @ 5:6e589f267c14
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| author | devteam |
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| date | Tue, 04 Nov 2014 12:15:19 -0500 |
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| 4:619e0fcd9126 | 5:6e589f267c14 |
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| 1 A collection of tools for converting genome annotation between GTF (Gene Transfer Format), | |
| 2 BED (Browser Extensible Data) and GFF (Generic Feature Format). | |
| 3 | |
| 4 INTRODUCTION | |
| 5 | |
| 6 Several genome annotation centers provide their data in GTF, BED, GFF3 etc. I have few programs | |
| 7 they mainly deals with converting between GTF, BED and GFF3 formats. They are extensively tested | |
| 8 with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. Please follow the | |
| 9 instructions below to clone these tools into your galaxy instance. | |
| 10 | |
| 11 CONTENTS | |
| 12 | |
| 13 Tool configuration files in *.xml format. | |
| 14 | |
| 15 gtf_to_gff.xml | |
| 16 gff_to_gtf.xml | |
| 17 bed_to_gff.xml | |
| 18 gff_to_bed.xml | |
| 19 gbk_to_gff.xml | |
| 20 gff_fmap.xml | |
| 21 | |
| 22 Python based scripts. | |
| 23 | |
| 24 gtf_to_gff.py: convert data from GTF to valid GFF3. | |
| 25 gff_to_gtf.py: convert data from GFF3 to GTF. | |
| 26 bed_to_gff.py: convert data from a 12 column UCSC wiggle BED format to GFF3. | |
| 27 gff_to_bed.py: convert gene transcript annotation from GFF3 to UCSC wiggle 12 column BED format. | |
| 28 gbk_to_gff.py: convert data from genbank format to GFF. | |
| 29 gff_fmap.py: find the relation between different features described in a GFF file. | |
| 30 GFFParser.py: Parse GFF/GTF files. | |
| 31 helper.py: Utility functions. | |
| 32 | |
| 33 test-data: Test data set. (move to your galaxy_root_folder/test-data/) | |
| 34 | |
| 35 You may need to move the test files into your test-data directory so galaxy can find them. | |
| 36 If you want to run the functional tests eg as: | |
| 37 | |
| 38 exmaple: | |
| 39 sh run_functional_tests.sh -id fml_gtf2gff | |
| 40 | |
| 41 REQUIREMENTS | |
| 42 | |
| 43 python | |
| 44 | |
| 45 COMMENTS/QUESTIONS | |
| 46 | |
| 47 I can be reached at vipin [at] cbio.mskcc.org | |
| 48 | |
| 49 LICENSE | |
| 50 | |
| 51 Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society | |
| 52 2013-2014 Memorial Sloan Kettering Cancer Center | |
| 53 | |
| 54 This program is free software; you can redistribute it and/or modify | |
| 55 it under the terms of the GNU General Public License as published by | |
| 56 the Free Software Foundation; either version 3 of the License, or | |
| 57 (at your option) any later version. | |
| 58 | |
| 59 COURTESY | |
| 60 | |
| 61 To the Galaxy Team. |