annotate smart_toolShed/SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervals.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#! /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
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# economic rights, and the successive licensors have only limited
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import os, struct, time
from optparse import OptionParser
from commons.core.parsing.ParserChooser import ParserChooser
from SMART.Java.Python.structure.Transcript import Transcript
from SMART.Java.Python.ncList.NCList import NCList
from SMART.Java.Python.ncList.NCListCursor import NCListCursor
from SMART.Java.Python.ncList.NCListFilePickle import NCListFilePickle, NCListFileUnpickle
from SMART.Java.Python.ncList.FileSorter import FileSorter
from SMART.Java.Python.misc.Progress import Progress
from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
from SMART.Java.Python.ncList.NCListCursor import NCListCursor
from SMART.Java.Python.ncList.FindOverlapsWithOneInterval import FindOverlapsWithOneInterval

REFERENCE = 0
QUERY = 1
TYPETOSTRING = {0: "reference", 1: "query"}

class FindOverlapsWithSeveralIntervals(object):
    
    def __init__(self, verbosity = 1):
        self._parsers            = {}
        self._outputFileName     = "outputOverlaps.gff3"
        self._iWriter            = None
        self._nbLines            = {REFERENCE: 0, QUERY: 0}
        self._verbosity          = verbosity
        self._ncLists            = {}
        self._sortedRefFileNames = None
        self._transQueryFileName = None
        self._cursors            = {}
        self._iFowoi             = FindOverlapsWithOneInterval(self._verbosity)
        
    def __del__(self):
        self.close()
        for fileName in (self._sortedRefFileNames, self._transQueryFileName):
            if os.path.exists(fileName):
                os.remove(fileName)
    
    def close(self):
        self._iFowoi.close()
        
    def setRefFileName(self, fileName, format):
        self.setFileName(fileName, format, REFERENCE)
        self._sortedRefFileNames = "%s_ref_sorted.pkl" % (os.path.splitext(fileName)[0])
        
    def setQueryFileName(self, fileName, format):
        self.setFileName(fileName, format, QUERY)
        self._transQueryFileName = "%s_query_trans.pkl" % (os.path.splitext(fileName)[0])

    def setFileName(self, fileName, format, type):
        chooser = ParserChooser(self._verbosity)
        chooser.findFormat(format)
        self._parsers[type]   = chooser.getParser(fileName)
        
    def setOutputFileName(self, outputFileName):
        self._iFowoi.setOutputFileName(outputFileName)

    def _sortRefFile(self):
        fs = FileSorter(self._parsers[REFERENCE], self._verbosity-4)
        fs.perChromosome(True)
        fs.setOutputFileName(self._sortedRefFileNames)
        fs.sort()
        self._nbLines[REFERENCE]      = fs.getNbElements()
        self._nbRefLinesPerChromosome = fs.getNbElementsPerChromosome()
        self._splittedFileNames       = fs.getOutputFileNames()

    def _translateQueryFile(self):
        pickler = NCListFilePickle(self._transQueryFileName, self._verbosity)
        progress = UnlimitedProgress(1000, "Translating query data", self._verbosity-4)
        cpt      = 0
        for queryTranscript in self._parsers[QUERY].getIterator():
            pickler.addTranscript(queryTranscript)
            progress.inc()
            cpt += 1
        progress.done()
        self._nbLines[QUERY] = cpt
        self._parsers[QUERY] = NCListFileUnpickle(self._transQueryFileName, self._verbosity)
            
    def prepareIntermediateFiles(self):
        self._sortRefFile()
        self._translateQueryFile()

    def createNCLists(self):
        self._ncLists = {}
        self._indices = {}
        self._cursors = {}
        for chromosome, fileName in self._splittedFileNames.iteritems():
            if self._verbosity > 3:
                print "  chromosome %s" % (chromosome)
            ncList = NCList(self._verbosity)
            ncList.createIndex(True)
            ncList.setChromosome(chromosome)
            ncList.setFileName(fileName)
            ncList.setNbElements(self._nbRefLinesPerChromosome[chromosome])
            ncList.buildLists()
            self._ncLists[chromosome] = ncList
            cursor = NCListCursor(None, ncList, 0, self._verbosity)
            self._cursors[chromosome] = cursor
            self._indices[chromosome] = ncList.getIndex()
        endTime = time.time()

    def compare(self):
        progress = Progress(self._nbLines[QUERY], "Comparing data", self._verbosity-3)
        startTime = time.time()
        for cpt, queryTranscript in enumerate(self._parsers[QUERY].getIterator()):
            chromosome = queryTranscript.getChromosome()
            if chromosome not in self._ncLists:
                continue
            self._iFowoi.setNCList(self._ncLists[chromosome], self._indices[chromosome])
            self._iFowoi.setTranscript(queryTranscript)
            self._iFowoi.compare()
            self._iFowoi.dumpWriter()
            progress.inc()
        progress.done()
        endTime = time.time()
        self._timeSpent = endTime - startTime

    def run(self):
        startTime = time.time()
        if self._verbosity > 2:
            print "Creating NC-list..."
        self.prepareIntermediateFiles()
        self.createNCLists()
        endTime = time.time()
        if self._verbosity > 2:
            print "    ...done (%.2gs)" % (endTime - startTime)
        self.compare()
        self.close()
        if self._verbosity > 0:
            print "# queries: %d" % (self._nbLines[QUERY])
            print "# refs:    %d" % (self._nbLines[REFERENCE])
            print "# written: %d (%d overlaps)" % (self._iFowoi._nbWritten, self._iFowoi._nbOverlaps)
            print "time:      %.2gs" % (self._timeSpent)


if __name__ == "__main__":
    description = "FindOverlaps With Several Intervals v1.0.0: Finds overlaps with several query intervals. [Category: Data comparison]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--query",       dest="inputQueryFileName", action="store",            type="string",  help="Query input file [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--queryFormat", dest="queryFormat",        action="store",            type="string",  help="format of previous file [compulsory] [format: transcript file format]")
    parser.add_option("-j", "--ref",         dest="inputRefFileName",   action="store",            type="string",  help="Reference input file [compulsory] [format: file in transcript format given by -g]")
    parser.add_option("-g", "--refFormat",   dest="refFormat",          action="store",            type="string",  help="format of previous file [compulsory] [format: transcript 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("-v", "--verbosity",   dest="verbosity",          action="store", default=1, type="int",     help="Trace level [format: int] [default: 1]")
    (options, args) = parser.parse_args()
    
    iFWSI = FindOverlapsWithSeveralIntervals(options.verbosity)
    iFWSI.setRefFileName(options.inputRefFileName, options.refFormat)
    iFWSI.setQueryFileName(options.inputQueryFileName, options.queryFormat)
    iFWSI.setOutputFileName(options.outputFileName)
    iFWSI.run()