Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/getIntrons.py @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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1 #! /usr/bin/env python
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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2 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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3 # Copyright INRA-URGI 2009-2010
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4 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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5 # This software is governed by the CeCILL license under French law and
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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6 # abiding by the rules of distribution of free software. You can use,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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7 # modify and/ or redistribute the software under the terms of the CeCILL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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9 # "http://www.cecill.info".
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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10 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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11 # As a counterpart to the access to the source code and rights to copy,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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12 # modify and redistribute granted by the license, users are provided only
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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13 # with a limited warranty and the software's author, the holder of the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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14 # economic rights, and the successive licensors have only limited
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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15 # liability.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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16 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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17 # In this respect, the user's attention is drawn to the risks associated
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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18 # with loading, using, modifying and/or developing or reproducing the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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19 # software by the user in light of its specific status of free software,
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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20 # that may mean that it is complicated to manipulate, and that also
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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21 # therefore means that it is reserved for developers and experienced
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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22 # professionals having in-depth computer knowledge. Users are therefore
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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23 # encouraged to load and test the software's suitability as regards their
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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24 # requirements in conditions enabling the security of their systems and/or
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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25 # data to be ensured and, more generally, to use and operate it in the
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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26 # same conditions as regards security.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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27 #
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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28 # The fact that you are presently reading this means that you have had
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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29 # knowledge of the CeCILL license and that you accept its terms.
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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30 #
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31 from optparse import OptionParser
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32 from commons.core.parsing.ParserChooser import ParserChooser
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 from commons.core.writer.TranscriptWriter import TranscriptWriter
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34 from SMART.Java.Python.structure.Transcript import Transcript
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35 from SMART.Java.Python.misc.Progress import Progress
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36
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37 class GetIntrons(object):
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38
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39 def __init__(self, verbosity):
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40 self.verbosity = verbosity
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41
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42 def setInputFile(self, fileName, format):
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43 chooser = ParserChooser(self.verbosity)
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44 chooser.findFormat(format)
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45 self.parser = chooser.getParser(fileName)
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46
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47 def setOutputFile(self, fileName):
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48 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
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49
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50 def run(self):
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51 progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
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52 nbIntrons = 0
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53 for cpt1, transcript in enumerate(self.parser.getIterator()):
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54 for cpt2, intron in enumerate(transcript.getIntrons()):
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55 intronTranscript = Transcript()
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56 intronTranscript.copy(intron)
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57 if "Parent" in intronTranscript.tags:
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58 del intronTranscript.tags["Parent"]
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59 intronTranscript.tags["feature"] = "transcript"
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60 if "ID" not in intronTranscript.tags or intronTranscript.tags["ID"] == "unnamed transcript":
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61 intronTranscript.tags["ID"] = "intron_%d-%d" % (cpt1+1, cpt2+1)
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62 if intronTranscript.getName() == "unnamed transcript":
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63 intronTranscript.setName("intron_%d-%d" % (cpt1+1, cpt2+1))
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64 self.writer.addTranscript(intronTranscript)
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65 nbIntrons += 1
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66 progress.inc()
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67 self.writer.write()
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68 self.writer.close()
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69 progress.done()
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70 if self.verbosity > 1:
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71 print "%d transcripts read" % (self.parser.getNbTranscripts())
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72 print "%d introns written" % (nbIntrons)
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73
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74
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75 if __name__ == "__main__":
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76
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77 description = "Get Introns v1.0.1: Get the introns of a set of transcripts. [Category: Data Modification]"
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78
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79 parser = OptionParser(description = description)
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80 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
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81 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
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82 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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83 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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84 (options, args) = parser.parse_args()
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85
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86 gi = GetIntrons(options.verbosity)
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87 gi.setInputFile(options.inputFileName, options.format)
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88 gi.setOutputFile(options.outputFileName)
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89 gi.run()