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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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3
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4 INTRODUCTION
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5
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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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10
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11 CONTENTS
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12
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13 Tool configuration files in *.xml format.
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14
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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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20 gff_fmap.xml
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21
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22 Python based scripts.
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23
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24 gtf_to_gff.py: convert data from GTF to valid GFF3.
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25 gff_to_gtf.py: convert data from GFF3 to GTF.
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26 bed_to_gff.py: convert data from a 12 column UCSC wiggle BED format to GFF3.
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27 gff_to_bed.py: convert gene transcript annotation from GFF3 to UCSC wiggle 12 column BED format.
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28 gbk_to_gff.py: convert data from genbank format to GFF.
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29 gff_fmap.py: find the relation between different features described in a GFF file.
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30 GFFParser.py: Parse GFF/GTF files.
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31 helper.py: Utility functions.
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32
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33 test-data: Test data set. (move to your galaxy_root_folder/test-data/)
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34
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35 You may need to move the test files into your test-data directory so galaxy can find them.
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36 If you want to run the functional tests eg as:
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37
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38 exmaple:
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39 sh run_functional_tests.sh -id fml_gtf2gff
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40
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41 REQUIREMENTS
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42
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43 python
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44
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45 COMMENTS/QUESTIONS
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46
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47 I can be reached at vipin [at] cbio.mskcc.org
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48
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49 LICENSE
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50
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51 Copyright (C) 2009-2012 Friedrich Miescher Laboratory of the Max Planck Society
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52 2013-2014 Memorial Sloan Kettering Cancer Center
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53
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54 This program is free software; you can redistribute it and/or modify
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55 it under the terms of the GNU General Public License as published by
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56 the Free Software Foundation; either version 3 of the License, or
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57 (at your option) any later version.
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58
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59 COURTESY
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60
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61 To the Galaxy Team.
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