Mercurial > repos > yufei-luo > s_mart

annotate smart_toolShed/SMART/Java/Python/convertTranscriptFile.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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children
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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 #
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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.
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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.
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27 #
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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 """
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32 Read a transcript file and convert it to another format
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33 """
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34
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35 import os, re
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36 from optparse import OptionParser
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37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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38 from commons.core.writer.TranscriptWriter import TranscriptWriter
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39 from SMART.Java.Python.misc.Progress import Progress
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40
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41
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42 class ConvertTranscriptFile(object):
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43 def __init__(self,inputFileName="", inputFormat ="", outputFileName="", outputFormat="", name="", sequenceFileName=None, strands=False, galaxy=False, feature=None, featurePart=None, verbosity=1):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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44 self.inputFileName = inputFileName
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45 self.inputFormat = inputFormat
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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46 self.outputFileName = outputFileName
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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47 self.outputFormat = outputFormat
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 self.name = name
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49 self.sequenceFileName = sequenceFileName
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50 self.strands = strands
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51 self.galaxy = galaxy
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52
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53 self.feature=feature
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54 self.featurePart=featurePart
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55
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56 self.verbosity = verbosity
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57
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58 def setAttributesFromCmdLine(self):
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59 description = "Convert Transcript File v1.0.3: Convert a file from a format to another. [Category: Conversion]"
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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60 parser = OptionParser(description = description)
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61 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in format given by -f]")
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62 parser.add_option("-f", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript or mapping file format]")
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63 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in format given by -g]")
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64 parser.add_option("-g", "--outputFormat", dest="outputFormat", action="store", type="string", help="format of the output file [compulsory] [format: transcript file format]")
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65 parser.add_option("-n", "--name", dest="name", action="store", default="SMART", type="string", help="name for the transcripts [format: string] [default: SMART]")
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66 parser.add_option("-s", "--sequences", dest="sequenceFileName", action="store", default=None, type="string", help="give the corresponding Multi-Fasta file (useful for EMBL format) [format: string]")
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67 parser.add_option("-t", "--strands", dest="strands", action="store_true", default=False, help="consider the 2 strands as different (only useful for writing WIG files) [format: bool] [default: False]")
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68 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
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69 parser.add_option("-G", "--galaxy", dest="galaxy", action="store_true", default=False, help="used for galaxy [format: bool] [default: False]")
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70 (options, args) = parser.parse_args()
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71 self._setAttributesFromOptions(options)
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72
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73 def _setAttributesFromOptions(self, options):
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74 self.inputFileName = options.inputFileName
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75 self.inputFormat = options.inputFormat
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76 self.outputFileName = options.outputFileName
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77 self.outputFormat = options.outputFormat
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78 self.name = options.name
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79 self.sequenceFileName = options.sequenceFileName
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80 self.strands = options.strands
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81 self.galaxy = options.galaxy
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82 self.verbosity = options.verbosity
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83
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84 def run(self):
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85 # create parser
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86 parser = TranscriptContainer(self.inputFileName, self.inputFormat, self.verbosity)
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87 # create writer
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88 writer = TranscriptWriter(self.outputFileName, self.outputFormat, self.verbosity)
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89 # connect parser and writer
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90 writer.setContainer(parser)
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91
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92 if self.name != None:
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93 writer.setTitle(self.name)
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94 if self.feature != None:
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95 writer.setFeature(self.feature)
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96 if self.featurePart != None:
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97 writer.setFeaturePart(self.featurePart)
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98 if self.sequenceFileName != None:
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99 writer.addSequenceFile(self.sequenceFileName)
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100
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101 nbItems = 0
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102 if self.verbosity > 0:
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103 nbItems = parser.getNbItems()
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104 print "%i items found" % (nbItems)
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105
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106 if self.strands:
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107 writer.setStrands(True)
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108 # convert
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109 writer.write()
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110 writer.close()
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111
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112 if __name__ == "__main__":
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113 iConvertTranscriptFile = ConvertTranscriptFile()
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114 iConvertTranscriptFile.setAttributesFromCmdLine()
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115 iConvertTranscriptFile.run()