annotate commons/core/parsing/CrossSsrAndBesMappedByBlatToGff.py @ 36:44d5973c188c

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# Copyright INRA (Institut National de la Recherche Agronomique)
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# http://urgi.versailles.inra.fr
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import os
import optparse
from commons.core.parsing.SsrParser import SsrParser
from commons.core.parsing.BlatParser import BlatParser

class CrossSsrAndBesMappedByBlatToGff(object):


    def __init__(self):
        self._inputFileSSR = ''
        self._inputFileBlat = ''
        self._outputFileGFF = ''
    
    def setAttributesFromCmdLine(self):
        help = '\
        \nThis Script Launch CrossSsrAndBesMappedByBlatToGff.\n\n\
        Example 1: python CrossSsrAndBesMappedByBlatToGff.py -s ssrResultsFile.tab -b blatResultsFile.tab -o outputFile.gff3\n\
        Example 2: python CrossSsrAndBesMappedByBlatToGff.py -s ssrResultsFile.tab -b blatResultsFile.tab -o outputFile.gff3 -n muscadine:filtre1\n\n'
        
        parser = optparse.OptionParser(usage= help, version="CovertSamToFastq.py v1.0")
        parser.add_option( '-s', '--ssr', dest='inputSSR', help='SSR Input File Name [Format: tabular]', default= None )
        parser.add_option( '-b', '--blat', dest='inputBLAT', help='Blat Input File Name [Format: tabular]', default= None )
        parser.add_option( '-o', '--output', dest='output', help='Output File Name [Format: GFF3]', default= None )
        parser.add_option( '-n', '--methodName', dest='methodName', help='Method name in col. 3 [Default: None]', default= None )
        ( options, args ) = parser.parse_args()
        self.options = options
    
    def checkOptions(self):
        if self.options.inputSSR == '':
            raise Exception("ERROR: No SSR file specified for -s !")
        elif not os.path.exists(self.options.inputSSR):
            raise Exception("ERROR: SSR Input File doesn't exist !")
        else:
            self._inputFileSSR = self.options.inputSSR
        
        if self.options.inputBLAT == '':
            raise Exception("ERROR: No Blat file specified for -b !")
        elif not os.path.exists(self.options.inputBLAT):
            raise Exception("ERROR: Blat Input File doesn't exist !")
        else:
            self._inputFileBlat = self.options.inputBLAT
            
        if self.options.output == '':
            raise Exception("ERROR: No Output file specified for -o !")
        else:
            self._outputFileGFF = self.options.output
            
        self._methodName = self.options.methodName
    
    def run(self):
        self.checkOptions()
        self._createGFFOutputFile()
        
        dictSsrParser = {}
        dictSsrParser = self.createDictOfSsrParser(dictSsrParser)
        
        BLATFile = open(self._inputFileBlat, 'r')
        
        headerBlatLine = BLATFile.readline()
        headerBlatLine = BLATFile.readline()
        headerBlatLine = BLATFile.readline()
        headerBlatLine = BLATFile.readline()
        headerBlatLine = BLATFile.readline()
        blatLine = BLATFile.readline()
        numberLine = 6
        while blatLine != '' and blatLine != '\n':
            thisBlatHit = BlatParser()
            thisBlatHit.setAttributesFromString(blatLine, numberLine)
            besName = thisBlatHit.getQName()
            
            if besName in dictSsrParser:
                lLinesToPrint = self.createListOfGFFLinesForThisBesWithSSR(thisBlatHit, dictSsrParser)
                self._printGFFLinesToOutputFile(lLinesToPrint)
            
            blatLine = BLATFile.readline()
            numberLine = numberLine + 1
        
        BLATFile.close()
        
    def createDictOfSsrParser(self, dictSsrParser):
        dictSsrParser = {}
        SSRFile = open(self._inputFileSSR, 'r')
        
        header = SSRFile.readline()
        line = SSRFile.readline()
        numberLine = 2
        
        while line != '' and line != '\n':
            thisSSRHit = SsrParser()
            thisSSRHit.setAttributesFromString(line, numberLine)
            
            BESName = thisSSRHit.getBesName()
            if not BESName in dictSsrParser:
                list = [thisSSRHit]
                dictSsrParser[BESName] = list
            else:
                list = dictSsrParser[BESName]
                list.append(thisSSRHit)
                dictSsrParser[BESName] = list
            
            line = SSRFile.readline()
            numberLine = numberLine + 1
            
        SSRFile.close()
        return dictSsrParser
    
    def createListOfGFFLinesForThisBesWithSSR(self, BlatHitObject, dictSsrParser):
        listGffLines = []
        
        besNameToKeep =  BlatHitObject.getQName()
        lOfSSRHitObject = dictSsrParser[besNameToKeep]
        
        for SSRHitObject in  lOfSSRHitObject:
            posSSRStart = self.convertSSRPositionsToChromPositions(SSRHitObject.getSsrStart(), BlatHitObject.getTStart(), BlatHitObject.getTEnd(), BlatHitObject.getStrand())
            posSSREnd = self.convertSSRPositionsToChromPositions(SSRHitObject.getSsrEnd(), BlatHitObject.getTStart(), BlatHitObject.getTEnd(), BlatHitObject.getStrand())
            ssrSeq = self.getSsrSeq(SSRHitObject.getSsrMotif(), SSRHitObject.getSsrMotifNumber())
            
            col1 = BlatHitObject.getTName()
            col2 = 'CrossSsrAndBesAlignedByBlat'
            if self._methodName != '' and self._methodName != None:
                col3 = '%s:SSR' %self._methodName
            else:
                col3 = 'SSR'
            col4 = posSSRStart
            col5 = posSSREnd
            col6 = '.'
            col7 = BlatHitObject.getStrand()
            col8 = '.'
            col9 = 'ID=SSR_%s_%s;Name=SSR_%s_%s;bes_name=%s;bes_size=%s;bes_matchstart=%s;bes_matchend=%s;bes_redundancy=%s;ssr_type=%s;ssr_motif=%s;ssr_motif_number=%s;ssr_start=%s;ssr_end=%s;muscadine_seq=%s' % (besNameToKeep, SSRHitObject.getBesRedundancy(), 
                                                                                                                                                                                           besNameToKeep, SSRHitObject.getBesRedundancy(),
                                                                                                                                                                                           besNameToKeep, BlatHitObject.getQSize(),
                                                                                                                                                                                           BlatHitObject.getQStart(), BlatHitObject.getQEnd(), 
                                                                                                                                                                                           SSRHitObject.getBesRedundancy(), SSRHitObject.getSsrNbNucleotides(),
                                                                                                                                                                                           SSRHitObject.getSsrMotif(), SSRHitObject.getSsrMotifNumber(),
                                                                                                                                                                                           SSRHitObject.getSsrStart(), SSRHitObject.getSsrEnd(), ssrSeq)
            gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9)
            listGffLines.append(gffLine)
            
        return listGffLines
    
    def convertSSRPositionsToChromPositions(self, ssrPos, chromPosStart, chromPosEnd, strand):
        if strand == '+':
            newPos =  int(chromPosStart) + int(ssrPos) - 1
        elif strand == '-':
            newPos =  int(chromPosEnd) - int(ssrPos) + 1
        return newPos
    
    def getSsrSeq(self, motif, nbMotif):
        ssrSeq = motif * int(nbMotif)
        return ssrSeq
    
    def _createGFFOutputFile(self):
        GFFfile = open(self._outputFileGFF, 'w')
        GFFfile.write("##gff-version 3\n")
        GFFfile.close()
        
    def _printGFFLinesToOutputFile(self, lLinesToPrint):
        GFFfile = open(self._outputFileGFF, 'a')
        for line in lLinesToPrint:
            GFFfile.write(line)
        GFFfile.close()

if __name__ == '__main__':
    iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff()
    iCrossSsrAndBesMappedByBlatToGff.setAttributesFromCmdLine()
    iCrossSsrAndBesMappedByBlatToGff.run()