annotate SMART/Java/Python/CollapseReads.py @ 24:452e051f6562

Deleted selected files

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 import os
32 from optparse import OptionParser, OptionGroup
33 from commons.core.parsing.ParserChooser import ParserChooser
34 from commons.core.writer.Gff3Writer import Gff3Writer
35 from SMART.Java.Python.structure.Transcript import Transcript
36 from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
37 from SMART.Java.Python.ncList.FileSorter import FileSorter
38 from SMART.Java.Python.misc.Progress import Progress
39 
40 
41 class CollapseReads(object):
42     """
43     Merge two reads if they have exactly the same genomic coordinates
44     """
45 
46     def __init__(self, verbosity = 0):
47         self.verbosity         = verbosity
48         self.inputReader       = None
49         self.outputWriter      = None
50         self.strands           = True
51         self.nbRead            = 0
52         self.nbWritten         = 0
53         self.nbMerges          = 0
54         self.splittedFileNames = {}
55 
56     def __del__(self):
57         for fileName in self.splittedFileNames.values():
58             os.remove(fileName)
59             
60     def close(self):
61         self.outputWriter.close()
62         
63     def setInputFile(self, fileName, format):
64         parserChooser = ParserChooser(self.verbosity)
65         parserChooser.findFormat(format)
66         self.parser = parserChooser.getParser(fileName)
67         self.sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0])
68 
69     def setOutputFile(self, fileName):
70         self.outputWriter = Gff3Writer(fileName, self.verbosity)
71 
72     def getNbElements(self):
73         return self.parser.getNbTranscripts()
74 
75     def _sortFile(self):
76         fs = FileSorter(self.parser, self.verbosity-4)
77         fs.perChromosome(True)
78         fs.setOutputFileName(self.sortedFileName)
79         fs.sort()
80         self.splittedFileNames       = fs.getOutputFileNames()
81         self.nbElementsPerChromosome = fs.getNbElementsPerChromosome()
82         self.nbRead                  = fs.getNbElements()
83         
84     def _iterate(self, chromosome):
85         progress    = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity)
86         transcripts = []
87         parser      = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)
88         for newTranscript in parser.getIterator():
89             newTranscripts = []
90             for oldTranscript in transcripts:
91                 if self._checkOverlap(newTranscript, oldTranscript):
92                     self._merge(newTranscript, oldTranscript)
93                 elif self._checkPassed(newTranscript, oldTranscript):
94                     self._write(oldTranscript)
95                 else:
96                     newTranscripts.append(oldTranscript)
97             newTranscripts.append(newTranscript)
98             transcripts = newTranscripts
99             progress.inc()
00         for transcript in transcripts:
01             self._write(transcript)
02         progress.done()
03 
04     def _merge(self, transcript1, transcript2):
05         self.nbMerges += 1
06         transcript2.setDirection(transcript1.getDirection())
07         transcript1.merge(transcript2)
08 
09     def _write(self, transcript):
10         self.nbWritten += 1
11         self.outputWriter.addTranscript(transcript)
12 
13     def _checkOverlap(self, transcript1, transcript2):
14         if transcript1.getStart() != transcript2.getStart() or transcript1.getEnd() != transcript2.getEnd():
15             return False
16         return (not self.strands or transcript1.getDirection() == transcript2.getDirection())
17 
18     def _checkPassed(self, transcript1, transcript2):
19         return (transcript2.getStart() < transcript1.getStart())
20 
21     def collapseChromosome(self, chromosome):
22         progress            = Progress(table.getNbElements(), "Analysing chromosome %s" % (chromosome), self.verbosity)
23         command             = "SELECT * FROM %s ORDER BY start ASC, end DESC" % (table.name)
24         transcriptStart     = None
25         transcriptEnd       = None
26         transcriptDirection = None
27         currentTranscript   = None
28         if self.strands:
29             command += ", direction"
30         for index, transcript in table.selectTranscripts(command, True):
31             self.nbRead += 1
32             if not self.strands:
33                 transcript.setDirection("+")
34             if transcriptStart != transcript.getStart() or transcriptEnd != transcript.getEnd() or transcriptDirection != transcript.getDirection():
35                 self.writeTranscript(currentTranscript)
36                 transcriptStart     = transcript.getStart()
37                 transcriptEnd       = transcript.getEnd()
38                 transcriptDirection = transcript.getDirection()
39                 currentTranscript   = transcript
40             else:
41                 currentTranscript.setTagValue("nbElements", (currentTranscript.getTagValue("nbElements") + 1) if "nbElements" in currentTranscript.getTagNames() else 1)
42             progress.inc()
43         self.writeTranscript(currentTranscript)
44         progress.done()
45 
46     def collapse(self):
47         self._sortFile()
48         for chromosome in sorted(self.nbElementsPerChromosome.keys()):
49             self._iterate(chromosome)
50         self.outputWriter.close()
51         if self.verbosity > 1:
52             print "# reads read: %d" % (self.nbRead)
53             print "# reads written: %d (%.2f%%)" % (self.nbWritten, float(self.nbWritten) / self.nbRead * 100)
54             print "# reads merges: %d" % (self.nbMerges)
55 
56 if __name__ == "__main__":
57     
58     # parse command line
59     description = "Collapse Reads v1.0.3: Merge two reads if they have exactly the same genomic coordinates. [Category: Merge]"
60 
61     parser = OptionParser(description = description)
62     parser.add_option("-i", "--input",     dest="inputFileName",  action="store",                     type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
63     parser.add_option("-f", "--format",    dest="format",         action="store",                     type="string", help="format of the file [compulsory] [format: mapping file format]")
64     parser.add_option("-o", "--output",    dest="outputFileName", action="store",                     type="string", help="output file [compulsory] [format: output file in GFF3 format]")
65     parser.add_option("-s", "--strands",   dest="strands",        action="store_true", default=False,                help="merge elements on 2 different strands [format: bool] [default: false]")
66     parser.add_option("-v", "--verbosity", dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [default: 1] [format: int]")
67     (options, args) = parser.parse_args()
68 
69     collapser = CollapseReads(options.verbosity)
70     collapser.setInputFile(options.inputFileName, options.format)
71     collapser.setOutputFile(options.outputFileName)
72     collapser.strands = not options.strands
73     collapser.collapse()
74     collapser.close()