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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 from optparse import OptionParser
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32 from commons.core.parsing.ParserChooser import ParserChooser
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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 RemoveExons(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 self.selection = False
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42
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43 def setInputFile(self, fileName, format):
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44 chooser = ParserChooser(self.verbosity)
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45 chooser.findFormat(format)
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46 self.parser = chooser.getParser(fileName)
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47
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48 def setOutputFile(self, fileName):
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49 self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
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50
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51 def run(self):
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52 progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
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53 for transcript in self.parser.getIterator():
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54 transcript.removeExons()
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55 self.writer.addTranscript(transcript)
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56 progress.inc()
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57 self.writer.write()
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58 self.writer.close()
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59 progress.done()
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60
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61 if __name__ == "__main__":
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62
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63 description = "Remove Exons v1.0.1: Excluse the exons of a set of transcripts. [Category: Data Modification]"
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64
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65 parser = OptionParser(description = description)
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66 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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67 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
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68 parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]")
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69 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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70 (options, args) = parser.parse_args()
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71
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72 re = RemoveExons(options.verbosity)
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73 re.setInputFile(options.inputFileName, options.format)
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74 re.setOutputFile(options.outputFileName)
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75 re.run()
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