Mercurial > repos > yufei-luo > s_mart
comparison smart_toolShed/SMART/Java/Python/findTss.py @ 0:e0f8dcca02ed
Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
| author | yufei-luo |
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| date | Thu, 17 Jan 2013 10:52:14 -0500 |
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| -1:000000000000 | 0:e0f8dcca02ed |
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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 """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 |