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annotate GFFtools-GX/README @ 3:ff2c2e6f4ab3

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Uploaded version 2.0.0 of gfftools ready to import to local instance
author vipints
date Wed, 11 Jun 2014 16:29:25 -0400
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1 A collection of tools for converting genome annotation between GTF (Gene Transfer Format),
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2 BED (Browser Extensible Data) and GFF (Generic Feature Format).
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4 INTRODUCTION
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6 Several genome annotation centers provide their data in GTF, BED, GFF3 etc. I have few programs
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7 they mainly deals with converting between GTF, BED and GFF3 formats. They are extensively tested
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8 with files from different centers like ENSEMBL, UCSC, JGI and NCBI AceView. Please follow the
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9 instructions below to clone these tools into your galaxy instance.
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11 CONTENTS
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13 Tool configuration files in *.xml format.
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15 gtf_to_gff.xml
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16 gff_to_gtf.xml
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17 bed_to_gff.xml
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18 gff_to_bed.xml
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19 gbk_to_gff.xml
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21 Python based scripts.
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23 gtf_to_gff.py: convert data from GTF to valid GFF3.
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24 gff_to_gtf.py: convert data from GFF3 to GTF.
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25 bed_to_gff.py: convert data from a 12 column UCSC wiggle BED format to GFF3.
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26 gff_to_bed.py: convert gene transcript annotation from GFF3 to UCSC wiggle 12 column BED format.
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27 gbk_to_gff.py: convert data from genbank format to GFF.
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28 GFFParser.py: Parse GFF/GTF files.
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29 helper.py: Utility functions.
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31 test-data: Test data set. (move to your galaxy_root_folder/test-data/)
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33 You may need to move the test files into your test-data directory so galaxy can find them.
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34 If you want to run the functional tests eg as:
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36 exmaple:
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37 sh run_functional_tests.sh -id fml_gtf2gff
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38
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39 REQUIREMENTS
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41 python
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43 COMMENTS/QUESTIONS
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45 I can be reached at vipin [at] cbio.mskcc.org
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47 LICENSE
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48
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49 Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society
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50 2013-2014 Memorial Sloan Kettering Cancer Center
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51
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52 This program is free software; you can redistribute it and/or modify
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53 it under the terms of the GNU General Public License as published by
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54 the Free Software Foundation; either version 3 of the License, or
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55 (at your option) any later version.
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57 COURTESY
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59 To the Galaxy Team.