annotate SMART/Java/Python/CountLoci.py @ 46:169d364ddd91

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#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2012
# 
# 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.
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# 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,
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import os, os.path, random
from optparse import OptionParser
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from commons.core.parsing.GffParser import GffParser
from commons.core.writer.Gff3Writer import Gff3Writer
from commons.core.writer.TranscriptWriter import TranscriptWriter
from SMART.Java.Python.misc.Progress import Progress
from SMART.Java.Python.misc.RPlotter import RPlotter
from SMART.Java.Python.cleanGff import CleanGff
from SMART.Java.Python.CompareOverlappingSmallRef import CompareOverlappingSmallRef
from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
from SMART.Java.Python.GetUpDownStream import GetUpDownStream

REFERENCE = 0
QUERY = 1

class CountLoci(object):
    
    def __init__(self, verbosity = 1):
        self.verbosity = verbosity
        self.tmpFileNames = []

    def __del__(self):
        for fileName in self.tmpFileNames:
            if os.path.exists(fileName):
                os.remove(fileName)
    
    def setInputFile(self, fileName, format):
        self.inputFileName = fileName
        self.inputFormat = format
        self.parser = TranscriptContainer(fileName, format, self.verbosity-1)
        if self.verbosity > 0:
            print "%d elements in input" % (self.parser.getNbTranscripts())

    def setReference(self, fileName):
        self.referenceFileName = fileName

    def setDistance(self, distance):
        self.distance = distance

    def setOutputFileName(self, fileName):
        self.outputFileName = fileName
        self.writer         = Gff3Writer(fileName, self.verbosity-1)
        self.outputBase     = "%s_%d_" % (os.path.splitext(fileName)[0], random.randint(0, 10000))

    def _writeTmpRef(self, tags, outputFileName):
        cleanGff = CleanGff(self.verbosity-1)
        cleanGff.setInputFileName(self.referenceFileName)
        cleanGff.setOutputFileName(outputFileName)
        cleanGff.setAcceptedTypes(tags)
        cleanGff.run()

    def _getReferenceFiles(self):
        self.referenceFiles = {"CDS":                       "%scds.gff3"      % (self.outputBase), \
                               "five_prime_UTR":            "%sfive.gff3"     % (self.outputBase), \
                               "three_prime_UTR":           "%sthree.gff3"    % (self.outputBase), \
                               "mRNA":                      "%smrna.gff3"     % (self.outputBase), \
                               "ncRNA":                     "%sncRNA.gff3"     % (self.outputBase), \
                               "transposable_element_gene": "%sTE.gff3"       % (self.outputBase), \
                               "vic":                       "%svicinity.gff3" % (self.outputBase)}
        self.tmpFileNames.extend(self.referenceFiles.values())
        for tag, fileName in self.referenceFiles.iteritems():
            if tag == "ncRNA":
                self._writeTmpRef(["miRNA", "ncRNA", "rRNA", "snoRNA", "snRNA", "tRNA"], fileName)
            elif tag == "vic":
                continue
            else:
                self._writeTmpRef([tag], fileName)

    def _compare(self, queryFileName, queryFormat, referenceFileName, referenceFormat, outputFileName, exclusion = False):
        co = CompareOverlappingSmallRef(self.verbosity-1)
        co.setQueryFile(queryFileName, queryFormat)
        co.setReferenceFile(referenceFileName, referenceFormat)
        co.setOutputFile(outputFileName)
        if exclusion:
            co.setInvert(True)
        co.run()
        return co.nbWritten

    def _copy(self, inputFile, tag):
        parser = GffParser(inputFile, self.verbosity-1)
        for transcript in parser.getIterator():
            transcript.setTagValue("locus", tag)
            self.writer.addTranscript(transcript)
        
    def _getCds(self):
        outputFileName   = "%sin_cds.gff3" % (self.outputBase)
        outputNoFileName = "%sin_nocds.gff3" % (self.outputBase)
        self.tmpFileNames.extend([outputFileName, outputNoFileName])
        nbOverlaps = self._compare(self.inputFileName, self.inputFormat, self.referenceFiles["CDS"], "gff3", outputFileName)
        self._compare(self.inputFileName, self.inputFormat, self.referenceFiles["CDS"], "gff3", outputNoFileName, True)
        self._copy(outputFileName, "CDS")
        if self.verbosity > 0:
            print "%d overlaps in CDS" % (nbOverlaps)
        return outputNoFileName

    def _getFivePrime(self, inputFileName):
        outputFileName   = "%sin_five.gff3" % (self.outputBase)
        outputNoFileName = "%sin_nofive.gff3" % (self.outputBase)
        self.tmpFileNames.extend([outputFileName, outputNoFileName])
        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["five_prime_UTR"], "gff3", outputFileName)
        self._compare(inputFileName, "gff3", self.referenceFiles["five_prime_UTR"], "gff3", outputNoFileName, True)
        self._copy(outputFileName, "five_prime_UTR")
        if self.verbosity > 0:
            print "%d overlaps in 5' UTR" % (nbOverlaps)
        return outputNoFileName
    
    def _getThreePrime(self, inputFileName):
        outputFileName   = "%sin_three.gff3" % (self.outputBase)
        outputNoFileName = "%sin_nothree.gff3" % (self.outputBase)
        self.tmpFileNames.extend([outputFileName, outputNoFileName])
        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["three_prime_UTR"], "gff3", outputFileName)
        self._compare(inputFileName, "gff3", self.referenceFiles["three_prime_UTR"], "gff3", outputNoFileName, True)
        self._copy(outputFileName, "three_prime_UTR")
        if self.verbosity > 0:
            print "%d overlaps in 3' UTR" % (nbOverlaps)
        return outputNoFileName
    
    def _getNcRna(self, inputFileName):
        outputFileName   = "%sin_ncRna.gff3" % (self.outputBase)
        outputNoFileName = "%sin_noNcRna.gff3" % (self.outputBase)
        self.tmpFileNames.extend([outputFileName, outputNoFileName])
        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["ncRNA"], "gff3", outputFileName)
        self._compare(inputFileName, "gff3", self.referenceFiles["ncRNA"], "gff3", outputNoFileName, True)
        self._copy(outputFileName, "ncRNA")
        if self.verbosity > 0:
            print "%d overlaps in ncRNA" % (nbOverlaps)
        return outputNoFileName
    
    def _getTe(self, inputFileName):
        outputFileName   = "%sin_te.gff3" % (self.outputBase)
        outputNoFileName = "%sin_noTe.gff3" % (self.outputBase)
        self.tmpFileNames.extend([outputFileName, outputNoFileName])
        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["transposable_element_gene"], "gff3", outputFileName)
        self._compare(inputFileName, "gff3", self.referenceFiles["transposable_element_gene"], "gff3", outputNoFileName, True)
        self._copy(outputFileName, "TE")
        if self.verbosity > 0:
            print "%d overlaps in TE" % (nbOverlaps)
        return outputNoFileName
    
    def _getIntron(self, inputFileName):
        outputFileName   = "%sin_intron.gff3" % (self.outputBase)
        outputNoFileName = "%sin_nointron.gff3" % (self.outputBase)
        self.tmpFileNames.extend([outputFileName, outputNoFileName])
        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["mRNA"], "gff3", outputFileName)
        self._compare(inputFileName, "gff3", self.referenceFiles["mRNA"], "gff3", outputNoFileName, True)
        self._copy(outputFileName, "intron")
        if self.verbosity > 0:
            print "%d overlaps in introns" % (nbOverlaps)
        return outputNoFileName
    
    def _getVicinity(self, inputFileName):
        guds = GetUpDownStream(self.verbosity-1)
        guds.setInputFile(self.referenceFiles["mRNA"], "gff3")
        guds.setOutputFile(self.referenceFiles["vic"])
        guds.setDistances(self.distance, self.distance)
        guds.run()
        outputFileName = "%sout_vicinity.gff3" % (self.outputBase)
        outputNoFileName = "%sout_novicinity.gff3" % (self.outputBase)
        self.tmpFileNames.extend([outputFileName, outputNoFileName])
        nbOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["vic"], "gff3", outputFileName)
        nbNoOverlaps = self._compare(inputFileName, "gff3", self.referenceFiles["vic"], "gff3", outputNoFileName, True)
        self._copy(outputFileName, "vicinity")
        self._copy(outputNoFileName, "intergenic")
        if self.verbosity > 0:
            print "%d overlaps in vicinity" % (nbOverlaps)
            print "%d elsewhere" % (nbNoOverlaps)
    
    def run(self):
        self._getReferenceFiles()
        outputFileName = self._getCds()
        outputFileName = self._getFivePrime(outputFileName)
        outputFileName = self._getThreePrime(outputFileName)
        outputFileName = self._getNcRna(outputFileName)
        outputFileName = self._getTe(outputFileName)
        outputFileName = self._getIntron(outputFileName)
        self._getVicinity(outputFileName)



if __name__ == "__main__":
    
    # parse command line
    description = "Count Loci v1.0.0: Count input elements with respect to CDS, 5' UTR, 3' UTR, intron, downstream, upstream. [Category: Personal]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",            type="string", help="input file              [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--format",    dest="format",         action="store",            type="string", help="format of the input     [compulsory] [format: transcript file format]")
    parser.add_option("-r", "--reference", dest="reference",      action="store",            type="string", help="reference file          [compulsory] [format: file in GFF 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("-d", "--distance",  dest="distance",       action="store",            type="int",    help="distance up/down stream [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]")
    (options, args) = parser.parse_args()

    cl = CountLoci(options.verbosity)
    cl.setInputFile(options.inputFileName, options.format)
    cl.setDistance(options.distance)
    cl.setReference(options.reference)
    cl.setOutputFileName(options.outputFileName)
    cl.run()