Mercurial > repos > vipints > fml_gff3togtf
comparison fml_gff_converter_programs/README @ 0:ed53dca1c6ff
Migrated tool version 1.0.0 from old tool shed archive to new tool shed repository
| author | vipints |
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| date | Tue, 07 Jun 2011 17:26:20 -0400 |
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| 1 A collection of tools for converting genome annotation between GTF (Gene Transfer Format), BED (Browser Extensible Data) and GFF (Generic Feature Format) | |
| 2 | |
| 3 INTRODUCTION | |
| 4 | |
| 5 Several genome annotation centers provide their data in GTF, BED, GFF3 etc. I have few programs | |
| 6 they mainly deals with converting between GTF, BED and GFF3 formats. They are extensively tested | |
| 7 with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. Please follow the | |
| 8 instructions below to clone these tools into your galaxy instance. | |
| 9 | |
| 10 CONTENTS | |
| 11 | |
| 12 galaxy: Contains tool configuration files in *.xml format. | |
| 13 | |
| 14 Tool configuration files. Please add right path to locate the scripts. | |
| 15 | |
| 16 gtf_to_gff3.xml | |
| 17 | |
| 18 gff3_to_gtf.xml | |
| 19 | |
| 20 bed_to_gff3.xml | |
| 21 | |
| 22 gff3_to_bed.xml | |
| 23 | |
| 24 t: Test data set. (move to your galaxy root folder/test-data/) | |
| 25 | |
| 26 You may need to move the test files into your test-data directory so galaxy can find them. | |
| 27 If you want to run the functional tests eg as: | |
| 28 | |
| 29 sh run_functional_tests.sh -id fml_gtf2gff3 | |
| 30 | |
| 31 scripts: Python based and Perl based scripts. | |
| 32 | |
| 33 gtf_to_gff3_converter.py: This tool converts data from GTF format to valid GFF3 format. | |
| 34 | |
| 35 gff3_to_gtf_converter.pl: This tool converts data from GFF3 format to GTF format. | |
| 36 | |
| 37 bed_to_gff3_converter.py: This tool converts data from a 12 column UCSC wiggle BED format to GFF3 format. | |
| 38 | |
| 39 gff3_to_bed_converter.py: This tool converts gene transcript annotation from GFF3 format to UCSC wiggle 12 column BED format. | |
| 40 | |
| 41 REQUIREMENTS | |
| 42 | |
| 43 Python, Perl and if you are interested to use gff3_to_gtf_converter.pl please install Bio::Perl module. | |
| 44 | |
| 45 COMMENTS/QUESTIONS | |
| 46 | |
| 47 I can be reached at vipin.ts@tuebingen.mpg.de | |
| 48 | |
| 49 LICENSE | |
| 50 | |
| 51 Copyright (C) 2010 Friedrich Miescher Laboratory of the Max Planck Society | |
| 52 | |
| 53 This program is free software; you can redistribute it and/or modify | |
| 54 it under the terms of the GNU General Public License as published by | |
| 55 the Free Software Foundation; either version 3 of the License, or | |
| 56 (at your option) any later version. | |
| 57 | |
| 58 COURTESY | |
| 59 | |
| 60 To the Galaxy Team. |