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annotate smart_toolShed/SMART/Java/Python/fold.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
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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".
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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 #
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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 mapping file (many formats supported) and select some of them
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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33 Mappings should be sorted by read names
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34 """
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35
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36 from optparse import OptionParser
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37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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38 from SMART.Java.Python.toolLauncher.RnaFoldLauncher import RnaFoldLauncher
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39 from commons.core.writer.Gff3Writer import Gff3Writer
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40
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41
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42 class Fold(object):
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43 """
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44 Fold a series of transcripts
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45 """
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46
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47 def __init__(self, verbosity = 0):
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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48 self.verbosity = verbosity
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49 self.rnaFoldLauncher = RnaFoldLauncher(verbosity)
e0f8dcca02ed Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
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50 self.gff3Writer = None
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51
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52
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53 def setInputFileName(self, fileName, format):
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54 transcriptContainer = TranscriptContainer(fileName, format, options.verbosity)
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55 self.rnaFoldLauncher.setTranscriptList(transcriptContainer)
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56
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57
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58 def setOutputFileName(self, fileName):
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59 self.gff3Writer = Gff3Writer("%s.gff3" % (fileName), self.verbosity)
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60
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61
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62 def setGenomeFileName(self, fileName):
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63 self.rnaFoldLauncher.setGenomeFile(fileName)
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65
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66 def setExtensions(self, fivePrime, threePrime):
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67 self.rnaFoldLauncher.setExtensions(fivePrime, threePrime)
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68
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69
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70 def start(self):
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71 self.gff3Writer.addTranscriptList(self.rnaFoldLauncher.getResults())
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72
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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 # parse command line
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78 description = "Fold v1.0.1: Fold a list of transcript and give the energy. [Category: Personal]"
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79
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80 parser = OptionParser(description = description)
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81 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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82 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
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83 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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84 parser.add_option("-g", "--genome", dest="genomeFileName", action="store", type="string", help="genome file name [format: file in FASTA format]")
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85 parser.add_option("-5", "--fivePrime", dest="fivePrime", action="store", type="int", help="extend towards the 5' end [format: int]")
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86 parser.add_option("-3", "--threePrime", dest="threePrime", action="store", type="int", help="extend towards the 3' end [format: int]")
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87 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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88 (options, args) = parser.parse_args()
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89
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90 folder = Fold(options.verbosity)
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91 folder.setInputFileName(options.inputFileName, options.format)
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92 folder.setOutputFileName(options.outputFileName)
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93 folder.setExtensions(options.fivePrime, options.threePrime)
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94 folder.setGenomeFileName(options.genomeFileName)
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95 folder.start()