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+ − 1 #! /usr/bin/env python
+ − 2 #
+ − 3 # Copyright INRA-URGI 2009-2010
+ − 4 #
+ − 5 # This software is governed by the CeCILL license under French law and
+ − 6 # abiding by the rules of distribution of free software. You can use,
+ − 7 # modify and/ or redistribute the software under the terms of the CeCILL
+ − 8 # license as circulated by CEA, CNRS and INRIA at the following URL
+ − 9 # "http://www.cecill.info".
+ − 10 #
+ − 11 # As a counterpart to the access to the source code and rights to copy,
+ − 12 # modify and redistribute granted by the license, users are provided only
+ − 13 # with a limited warranty and the software's author, the holder of the
+ − 14 # economic rights, and the successive licensors have only limited
+ − 15 # liability.
+ − 16 #
+ − 17 # In this respect, the user's attention is drawn to the risks associated
+ − 18 # with loading, using, modifying and/or developing or reproducing the
+ − 19 # software by the user in light of its specific status of free software,
+ − 20 # that may mean that it is complicated to manipulate, and that also
+ − 21 # therefore means that it is reserved for developers and experienced
+ − 22 # professionals having in-depth computer knowledge. Users are therefore
+ − 23 # encouraged to load and test the software's suitability as regards their
+ − 24 # requirements in conditions enabling the security of their systems and/or
+ − 25 # data to be ensured and, more generally, to use and operate it in the
+ − 26 # same conditions as regards security.
+ − 27 #
+ − 28 # The fact that you are presently reading this means that you have had
+ − 29 # knowledge of the CeCILL license and that you accept its terms.
+ − 30 #
+ − 31 """
+ − 32 Read a transcript file and convert it to another format
+ − 33 """
+ − 34
+ − 35 import os, re
+ − 36 from optparse import OptionParser
+ − 37 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 38 from commons.core.writer.TranscriptWriter import TranscriptWriter
+ − 39 from SMART.Java.Python.misc.Progress import Progress
+ − 40
+ − 41
+ − 42 class ConvertTranscriptFile(object):
+ − 43 def __init__(self,inputFileName="", inputFormat ="", outputFileName="", outputFormat="", name="", sequenceFileName=None, strands=False, galaxy=False, feature=None, featurePart=None, verbosity=1):
+ − 44 self.inputFileName = inputFileName
+ − 45 self.inputFormat = inputFormat
+ − 46 self.outputFileName = outputFileName
+ − 47 self.outputFormat = outputFormat
+ − 48 self.name = name
+ − 49 self.sequenceFileName = sequenceFileName
+ − 50 self.strands = strands
+ − 51 self.galaxy = galaxy
+ − 52
+ − 53 self.feature=feature
+ − 54 self.featurePart=featurePart
+ − 55
+ − 56 self.verbosity = verbosity
+ − 57
+ − 58 def setAttributesFromCmdLine(self):
+ − 59 description = "Convert Transcript File v1.0.3: Convert a file from a format to another. [Category: Conversion]"
+ − 60 parser = OptionParser(description = description)
+ − 61 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in format given by -f]")
+ − 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]")
+ − 63 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in format given by -g]")
+ − 64 parser.add_option("-g", "--outputFormat", dest="outputFormat", action="store", type="string", help="format of the output file [compulsory] [format: transcript file format]")
+ − 65 parser.add_option("-n", "--name", dest="name", action="store", default="SMART", type="string", help="name for the transcripts [format: string] [default: SMART]")
+ − 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]")
+ − 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]")
+ − 68 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]")
+ − 69 parser.add_option("-G", "--galaxy", dest="galaxy", action="store_true", default=False, help="used for galaxy [format: bool] [default: False]")
+ − 70 (options, args) = parser.parse_args()
+ − 71 self._setAttributesFromOptions(options)
+ − 72
+ − 73 def _setAttributesFromOptions(self, options):
+ − 74 self.inputFileName = options.inputFileName
+ − 75 self.inputFormat = options.inputFormat
+ − 76 self.outputFileName = options.outputFileName
+ − 77 self.outputFormat = options.outputFormat
+ − 78 self.name = options.name
+ − 79 self.sequenceFileName = options.sequenceFileName
+ − 80 self.strands = options.strands
+ − 81 self.galaxy = options.galaxy
+ − 82 self.verbosity = options.verbosity
+ − 83
+ − 84 def run(self):
+ − 85 # create parser
+ − 86 parser = TranscriptContainer(self.inputFileName, self.inputFormat, self.verbosity)
+ − 87 # create writer
+ − 88 writer = TranscriptWriter(self.outputFileName, self.outputFormat, self.verbosity)
+ − 89 # connect parser and writer
+ − 90 writer.setContainer(parser)
+ − 91
+ − 92 if self.name != None:
+ − 93 writer.setTitle(self.name)
+ − 94 if self.feature != None:
+ − 95 writer.setFeature(self.feature)
+ − 96 if self.featurePart != None:
+ − 97 writer.setFeaturePart(self.featurePart)
+ − 98 if self.sequenceFileName != None:
+ − 99 writer.addSequenceFile(self.sequenceFileName)
+ − 100
+ − 101 nbItems = 0
+ − 102 if self.verbosity > 0:
+ − 103 nbItems = parser.getNbItems()
+ − 104 print "%i items found" % (nbItems)
+ − 105
+ − 106 if self.strands:
+ − 107 writer.setStrands(True)
+ − 108 # convert
+ − 109 writer.write()
+ − 110 writer.close()
+ − 111
+ − 112 if __name__ == "__main__":
+ − 113 iConvertTranscriptFile = ConvertTranscriptFile()
+ − 114 iConvertTranscriptFile.setAttributesFromCmdLine()
+ − 115 iConvertTranscriptFile.run()