annotate SMART/Java/Python/ncList/FindOverlapsWithSeveralIntervals.py @ 6:769e306b7933

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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".
# 
# As a counterpart to the access to the source code and rights to copy,
# modify and redistribute granted by the license, users are provided only
# with a limited warranty and the software's author, the holder of the
# economic rights, and the successive licensors have only limited
# liability.
# 
# In this respect, the user's attention is drawn to the risks associated
# with loading, using, modifying and/or developing or reproducing the
# software by the user in light of its specific status of free software,
# that may mean that it is complicated to manipulate, and that also
# therefore means that it is reserved for developers and experienced
# professionals having in-depth computer knowledge. Users are therefore
# encouraged to load and test the software's suitability as regards their
# requirements in conditions enabling the security of their systems and/or
# data to be ensured and, more generally, to use and operate it in the
# same conditions as regards security.
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# The fact that you are presently reading this means that you have had
# knowledge of the CeCILL license and that you accept its terms.
#

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()