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author vipints <vipin@cbio.mskcc.org>
date Fri, 24 Apr 2015 18:04:27 -0400
parents c42c69aa81f8
children
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1 GFFtools-GX
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2 ===========
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4 A collection of tools for converting genome annotation between [GTF](https://genome.ucsc.edu/FAQ/FAQformat.html#format4), [BED](https://genome.ucsc.edu/FAQ/FAQformat.html#format1), [GenBank](http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html) and [GFF](https://genome.ucsc.edu/FAQ/FAQformat.html#format3).
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6 ##### INTRODUCTION
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8 Several genome annotation centers provide their data in GTF, BED, GFF and GenBank format. I have few programs, they mainly deals with converting between GTF, BED GenBank and GFF formats. They are extensively tested with files from different centers like [ENSEMBL](http://www.ensembl.org), [UCSC](https://genome.ucsc.edu/), [JGI](http://genome.jgi.doe.gov/) and [NCBI AceView](http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/HelpJan.html). These programs can be easily integrated into your galaxy instance.
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10 ##### CONTENTS
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12 Included utilities are:
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14 BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF
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15 GBK-to-GFF: convert data from genbank format to GFF
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16 GFF-to-BED: convert data from GFF to 12 column BED format
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17 GFF-to-GTF: convert data from GFF to GTF
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18 GTF-to-GFF: convert data from GTF to valid GFF
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20 test-data: Test data set. (move to your galaxy-root-folder/test-data/)
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22 You may need to move the test files into your test-data directory so galaxy can find them.
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23 If you want to run the functional tests eg as:
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25 exmaple:
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26 sh run_functional_tests.sh -id fml_gtf2gff
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28 ##### REQUIREMENTS
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30 python2.6 or 2.7 and biopython
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32 Galaxy should be able to automatically install biopython via Galaxy toolshed.
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34 ##### COMMENTS/QUESTIONS
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36 I can be reached at vipin [at] cbio.mskcc.org
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38 ##### LICENSE
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40 Copyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society
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42 2013-2015, Memorial Sloan Kettering Cancer Center
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43 Vipin T Sreedharan <vipin@cbio.mskcc.org>
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44 All rights reserved.
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46 Licensed under the BSD 2-Clause License: <http://opensource.org/licenses/BSD-2-Clause>
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48 Redistribution and use in source and binary forms, with or without
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49 modification, are permitted provided that the following conditions are met:
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51 * Redistributions of source code must retain the above copyright notice,
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52 this list of conditions and the following disclaimer.
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54 * Redistributions in binary form must reproduce the above copyright notice,
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55 this list of conditions and the following disclaimer in the documentation
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56 and/or other materials provided with the distribution.
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58 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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59 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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60 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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61 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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62 FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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63 DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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64 SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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65 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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66 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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67 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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69 ##### COURTESY
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71 To the Galaxy Team.