annotate SMART/Java/Python/CollapseReads.py @ 36:44d5973c188c

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#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2010
# 
# This software is governed by the CeCILL license under French law and
# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
# license as circulated by CEA, CNRS and INRIA at the following URL
# "http://www.cecill.info".
# 
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# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
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import os
from optparse import OptionParser, OptionGroup
from commons.core.parsing.ParserChooser import ParserChooser
from commons.core.writer.Gff3Writer import Gff3Writer
from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
from SMART.Java.Python.ncList.FileSorter import FileSorter
from SMART.Java.Python.misc.Progress import Progress


class CollapseReads(object):
    """
    Merge two reads if they have exactly the same genomic coordinates
    """

    def __init__(self, verbosity = 0):
        self.verbosity         = verbosity
        self.inputReader       = None
        self.outputWriter      = None
        self.strands           = True
        self.nbRead            = 0
        self.nbWritten         = 0
        self.nbMerges          = 0
        self.splittedFileNames = {}

    def __del__(self):
        for fileName in self.splittedFileNames.values():
            os.remove(fileName)
            
    def close(self):
        self.outputWriter.close()
        
    def setInputFile(self, fileName, format):
        parserChooser = ParserChooser(self.verbosity)
        parserChooser.findFormat(format)
        self.parser = parserChooser.getParser(fileName)
        self.sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0])

    def setOutputFile(self, fileName):
        self.outputWriter = Gff3Writer(fileName, self.verbosity)

    def getNbElements(self):
        return self.parser.getNbTranscripts()

    def _sortFile(self):
        fs = FileSorter(self.parser, self.verbosity-4)
        fs.perChromosome(True)
        fs.setOutputFileName(self.sortedFileName)
        fs.sort()
        self.splittedFileNames       = fs.getOutputFileNames()
        self.nbElementsPerChromosome = fs.getNbElementsPerChromosome()
        self.nbRead                  = fs.getNbElements()
        
    def _iterate(self, chromosome):
        progress    = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity)
        transcripts = []
        parser      = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)
        for newTranscript in parser.getIterator():
            newTranscripts = []
            for oldTranscript in transcripts:
                if self._checkOverlap(newTranscript, oldTranscript):
                    self._merge(newTranscript, oldTranscript)
                elif self._checkPassed(newTranscript, oldTranscript):
                    self._write(oldTranscript)
                else:
                    newTranscripts.append(oldTranscript)
            newTranscripts.append(newTranscript)
            transcripts = newTranscripts
            progress.inc()
        for transcript in transcripts:
            self._write(transcript)
        progress.done()

    def _merge(self, transcript1, transcript2):
        self.nbMerges += 1
        transcript2.setDirection(transcript1.getDirection())
        transcript1.merge(transcript2)

    def _write(self, transcript):
        self.nbWritten += 1
        self.outputWriter.addTranscript(transcript)

    def _checkOverlap(self, transcript1, transcript2):
        if transcript1.getStart() != transcript2.getStart() or transcript1.getEnd() != transcript2.getEnd():
            return False
        return (not self.strands or transcript1.getDirection() == transcript2.getDirection())

    def _checkPassed(self, transcript1, transcript2):
        return (transcript2.getStart() < transcript1.getStart())

    def collapseChromosome(self, chromosome):
        progress            = Progress(table.getNbElements(), "Analysing chromosome %s" % (chromosome), self.verbosity)
        command             = "SELECT * FROM %s ORDER BY start ASC, end DESC" % (table.name)
        transcriptStart     = None
        transcriptEnd       = None
        transcriptDirection = None
        currentTranscript   = None
        if self.strands:
            command += ", direction"
        for index, transcript in table.selectTranscripts(command, True):
            self.nbRead += 1
            if not self.strands:
                transcript.setDirection("+")
            if transcriptStart != transcript.getStart() or transcriptEnd != transcript.getEnd() or transcriptDirection != transcript.getDirection():
                self.writeTranscript(currentTranscript)
                transcriptStart     = transcript.getStart()
                transcriptEnd       = transcript.getEnd()
                transcriptDirection = transcript.getDirection()
                currentTranscript   = transcript
            else:
                currentTranscript.setTagValue("nbElements", (currentTranscript.getTagValue("nbElements") + 1) if "nbElements" in currentTranscript.getTagNames() else 1)
            progress.inc()
        self.writeTranscript(currentTranscript)
        progress.done()

    def collapse(self):
        self._sortFile()
        for chromosome in sorted(self.nbElementsPerChromosome.keys()):
            self._iterate(chromosome)
        self.outputWriter.close()
        if self.verbosity > 1:
            print "# reads read: %d" % (self.nbRead)
            print "# reads written: %d (%.2f%%)" % (self.nbWritten, float(self.nbWritten) / self.nbRead * 100)
            print "# reads merges: %d" % (self.nbMerges)

if __name__ == "__main__":
    
    # parse command line
    description = "Collapse Reads v1.0.3: Merge two reads if they have exactly the same genomic coordinates. [Category: Merge]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",                     type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
    parser.add_option("-f", "--format",    dest="format",         action="store",                     type="string", help="format of the file [compulsory] [format: mapping file format]")
    parser.add_option("-o", "--output",    dest="outputFileName", action="store",                     type="string", help="output file [compulsory] [format: output file in GFF3 format]")
    parser.add_option("-s", "--strands",   dest="strands",        action="store_true", default=False,                help="merge elements on 2 different strands [format: bool] [default: false]")
    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [default: 1] [format: int]")
    (options, args) = parser.parse_args()

    collapser = CollapseReads(options.verbosity)
    collapser.setInputFile(options.inputFileName, options.format)
    collapser.setOutputFile(options.outputFileName)
    collapser.strands = not options.strands
    collapser.collapse()
    collapser.close()