6
+ − 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 """Find TSS from short reads"""
+ − 32 import os
+ − 33 from optparse import OptionParser
+ − 34 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+ − 35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+ − 36 from commons.core.writer.Gff3Writer import Gff3Writer
+ − 37
+ − 38 if __name__ == "__main__":
+ − 39
+ − 40 # parse command line
+ − 41 description = "Find TSS v1.0.1: Find the transcription start site of a list of transcripts. [Category: Merge]"
+ − 42
+ − 43 parser = OptionParser(description = description)
+ − 44 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+ − 45 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
+ − 46 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+ − 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]")
+ − 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]")
+ − 49 parser.add_option("-e", "--colinear", dest="colinear", action="store_true", default=False, help="group by strand [format: bool] [default: false]")
+ − 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]")
+ − 51 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+ − 52 (options, args) = parser.parse_args()
+ − 53
+ − 54 transcriptContainer = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+ − 55 transcriptListComparator = TranscriptListsComparator(None, options.verbosity)
+ − 56 transcriptListComparator.restrictToStart(transcriptListComparator.QUERY, 1)
+ − 57 transcriptListComparator.setMaxDistance(options.distance)
+ − 58 transcriptListComparator.aggregate(True)
+ − 59 transcriptListComparator.computeOdds(True)
+ − 60 transcriptListComparator.getColinearOnly(options.colinear)
+ − 61 transcriptListComparator.setNormalization(options.normalize)
+ − 62 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer)
+ − 63 transcriptListComparator.setOutputWriter(Gff3Writer(options.output, options.verbosity))
+ − 64 transcriptListComparator.compareTranscriptListSelfMerge()
+ − 65
+ − 66 if options.csv != None:
+ − 67 csvResults = transcriptListComparator.getOddsPerTranscript()
+ − 68 csvFile = open(options.csv, "w")
+ − 69 csvFile.write("Number,Transcript\n")
+ − 70 for number in sorted(list(set(csvResults.values()))):
+ − 71 csvFile.write("%d," % (number))
+ − 72 for name in csvResults:
+ − 73 if csvResults[name] == number:
+ − 74 csvFile.write("%s " % (name))
+ − 75 csvFile.write("\n")
+ − 76 csvFile.close()
+ − 77