annotate SMART/Java/Python/findTss.py @ 60:90f4b29d884f

Uploaded
author m-zytnicki
date Fri, 21 Feb 2014 08:32:36 -0500
parents 769e306b7933
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
1 #! /usr/bin/env python
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
2 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
3 # Copyright INRA-URGI 2009-2010
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
4 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
5 # This software is governed by the CeCILL license under French law and
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
6 # abiding by the rules of distribution of free software. You can use,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
7 # modify and/ or redistribute the software under the terms of the CeCILL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
8 # license as circulated by CEA, CNRS and INRIA at the following URL
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
9 # "http://www.cecill.info".
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
10 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
11 # As a counterpart to the access to the source code and rights to copy,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
12 # modify and redistribute granted by the license, users are provided only
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
13 # with a limited warranty and the software's author, the holder of the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
14 # economic rights, and the successive licensors have only limited
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
15 # liability.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
16 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
17 # In this respect, the user's attention is drawn to the risks associated
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
18 # with loading, using, modifying and/or developing or reproducing the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
19 # software by the user in light of its specific status of free software,
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
20 # that may mean that it is complicated to manipulate, and that also
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
21 # therefore means that it is reserved for developers and experienced
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
22 # professionals having in-depth computer knowledge. Users are therefore
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
23 # encouraged to load and test the software's suitability as regards their
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
24 # requirements in conditions enabling the security of their systems and/or
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
25 # data to be ensured and, more generally, to use and operate it in the
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
26 # same conditions as regards security.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
27 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
28 # The fact that you are presently reading this means that you have had
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
29 # knowledge of the CeCILL license and that you accept its terms.
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
30 #
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
31 """Find TSS from short reads"""
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
32 import os
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
33 from optparse import OptionParser
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
34 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
35 from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
36 from commons.core.writer.Gff3Writer import Gff3Writer
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
37
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
38 if __name__ == "__main__":
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
39
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
40 # parse command line
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
41 description = "Find TSS v1.0.1: Find the transcription start site of a list of transcripts. [Category: Merge]"
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
42
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
43 parser = OptionParser(description = description)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
44 parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
45 parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
46 parser.add_option("-o", "--output", dest="output", action="store", default=None, type="string", help="output file [compulsory] [format: output file in GFF3 format]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
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]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
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]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
49 parser.add_option("-e", "--colinear", dest="colinear", action="store_true", default=False, help="group by strand [format: bool] [default: false]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
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]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
51 parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
52 (options, args) = parser.parse_args()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
53
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
54 transcriptContainer = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
55 transcriptListComparator = TranscriptListsComparator(None, options.verbosity)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
56 transcriptListComparator.restrictToStart(transcriptListComparator.QUERY, 1)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
57 transcriptListComparator.setMaxDistance(options.distance)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
58 transcriptListComparator.aggregate(True)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
59 transcriptListComparator.computeOdds(True)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
60 transcriptListComparator.getColinearOnly(options.colinear)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
61 transcriptListComparator.setNormalization(options.normalize)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
62 transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer)
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
63 transcriptListComparator.setOutputWriter(Gff3Writer(options.output, options.verbosity))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
64 transcriptListComparator.compareTranscriptListSelfMerge()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
65
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
66 if options.csv != None:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
67 csvResults = transcriptListComparator.getOddsPerTranscript()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
68 csvFile = open(options.csv, "w")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
69 csvFile.write("Number,Transcript\n")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
70 for number in sorted(list(set(csvResults.values()))):
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
71 csvFile.write("%d," % (number))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
72 for name in csvResults:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
73 if csvResults[name] == number:
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
74 csvFile.write("%s " % (name))
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
75 csvFile.write("\n")
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
76 csvFile.close()
769e306b7933 Change the repository level.
yufei-luo
parents:
diff changeset
77