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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 """Find TSS from short reads"""
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32 import os
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33 from optparse import OptionParser
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34 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
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35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
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36 from commons.core.writer.Gff3Writer import Gff3Writer
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37
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38 if __name__ == "__main__":
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39
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40 # parse command line
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41 description = "Find TSS v1.0.1: Find the transcription start site of a list of transcripts. [Category: Merge]"
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42
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43 parser = OptionParser(description = description)
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44 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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45 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
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46 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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47 parser.add_option("-n", "--normalize", dest="normalize", action="store_true", default=False, help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [default: false]")
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48 parser.add_option("-d", "--distance", dest="distance", action="store", default=10, type="int", help="distance between two reads to mark the same TSS [format: int] [default: 10]")
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49 parser.add_option("-e", "--colinear", dest="colinear", action="store_true", default=False, help="group by strand [format: bool] [default: false]")
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50 parser.add_option("-c", "--csv", dest="csv", action="store", default=None, type="string", help="output a CSV file in the given path [format: output file in Excel format]")
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51 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
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52 (options, args) = parser.parse_args()
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53
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54 transcriptContainer = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
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55 transcriptListComparator = TranscriptListsComparator(None, options.verbosity)
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56 transcriptListComparator.restrictToStart(transcriptListComparator.QUERY, 1)
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57 transcriptListComparator.setMaxDistance(options.distance)
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58 transcriptListComparator.aggregate(True)
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59 transcriptListComparator.computeOdds(True)
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60 transcriptListComparator.getColinearOnly(options.colinear)
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61 transcriptListComparator.setNormalization(options.normalize)
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62 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer)
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63 transcriptListComparator.setOutputWriter(Gff3Writer(options.output, options.verbosity))
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64 transcriptListComparator.compareTranscriptListSelfMerge()
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65
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66 if options.csv != None:
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67 csvResults = transcriptListComparator.getOddsPerTranscript()
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68 csvFile = open(options.csv, "w")
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69 csvFile.write("Number,Transcript\n")
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70 for number in sorted(list(set(csvResults.values()))):
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71 csvFile.write("%d," % (number))
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72 for name in csvResults:
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73 if csvResults[name] == number:
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74 csvFile.write("%s " % (name))
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75 csvFile.write("\n")
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76 csvFile.close()
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77
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