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1 #! /usr/bin/env python
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2 #
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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
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6 # abiding by the rules of distribution of free software. You can use,
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7 # modify and/ or redistribute the software under the terms of the CeCILL
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8 # license as circulated by CEA, CNRS and INRIA at the following URL
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9 # "http://www.cecill.info".
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10 #
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11 # As a counterpart to the access to the source code and rights to copy,
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12 # modify and redistribute granted by the license, users are provided only
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13 # with a limited warranty and the software's author, the holder of the
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14 # economic rights, and the successive licensors have only limited
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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
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18 # with loading, using, modifying and/or developing or reproducing the
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19 # software by the user in light of its specific status of free software,
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20 # that may mean that it is complicated to manipulate, and that also
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21 # therefore means that it is reserved for developers and experienced
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22 # professionals having in-depth computer knowledge. Users are therefore
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23 # encouraged to load and test the software's suitability as regards their
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24 # requirements in conditions enabling the security of their systems and/or
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25 # data to be ensured and, more generally, to use and operate it in the
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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
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29 # knowledge of the CeCILL license and that you accept its terms.
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30 #
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31
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32
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33 """Convert files with some mapping format to coordinates format"""
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34
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35 import os
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36 from optparse import OptionParser
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37 from commons.core.parsing.PslParser import PslParser
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38 from commons.core.parsing.AxtParser import AxtParser
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39 from commons.core.writer.Gff3Writer import Gff3Writer
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40 from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
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41 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
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42 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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43 from SMART.Java.Python.misc.Progress import Progress
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44
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45
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46 class MappingToCoordinates(object):
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47 def __init__(self,verbosity=1, inputFileName=None, format = None, output=None,galaxy = False, title="S-MART"):
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48 self.verbosity = verbosity
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49 self.inputFileName = inputFileName
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50 self.format = format
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51 self.output = output
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52 self.galaxy = galaxy
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53 self.title = title
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54
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55 def setAttributesFromCmdLine(self):
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56 description = "Mapping To Coordinates v1.0.1: Convert a set of mappings (given by a mapping tool) to a set of transcripts. [Category: Conversion]"
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57 parser = OptionParser(description = description)
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58 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
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59 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: mapping file format]")
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60 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
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61 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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62 parser.add_option("-G", "--galaxy", dest="galaxy", action="store_true", default=False, help="used for galaxy [format: bool] [default: False]")
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63 (options, args) = parser.parse_args()
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64
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65 self.verbosity = options.verbosity
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66 self.inputFileName = options.inputFileName
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67 self.format = options.format
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68 self.output = options.output
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69 self.galaxy = options.galaxy
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70
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71 def run(self):
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72 if self.verbosity > 0:
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73 print "Reading input file..."
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74 parser = TranscriptContainer(self.inputFileName, self.format, self.verbosity)
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75 if self.verbosity > 0:
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76 print "... done"
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77 writer = Gff3Writer(self.output, self.verbosity, self.title)
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78
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79 progress = Progress(parser.getNbTranscripts(), "Reading %s" % (self.inputFileName), self.verbosity)
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80 for transcript in parser.getIterator():
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81 writer.addTranscript(transcript)
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82 progress.inc()
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83 progress.done()
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84
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85 if self.galaxy:
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86 os.rename("%s.gff3" % (self.output), self.output)
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87
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88 if __name__ == '__main__':
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89 launcher = MappingToCoordinates()
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90 launcher.setAttributesFromCmdLine()
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91 launcher.run()
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