view commons/core/parsing/VarscanFileForGnpSNP.py @ 36:44d5973c188c

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# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
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# This software is governed by the CeCILL license under French law and
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# 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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from commons.core.parsing.VarscanHitForGnpSNP import VarscanHitForGnpSNP
from commons.core.parsing.VarscanFile import VarscanFile

class VarscanFileForGnpSNP(VarscanFile):
    
    def __init__(self, varscanFileName, fastqFileName="", refFastaFileName="", taxonName=""):
        VarscanFile.__init__(self, varscanFileName)
        self._fastqFileName = fastqFileName
        self._refFastaFileName = refFastaFileName
        self._taxonName = taxonName
        self._previousVarscanHit = None
        
    ## Equal operator
    #
    # @param o a VarscanFileAnalysis instance
    #    
    def __eq__(self, o):
        return VarscanFile.__eq__(self, o) and self._fastqFileName == o._fastqFileName \
            and self._refFastaFileName == o._refFastaFileName and self._taxonName == o._taxonName
             
    def getVarscanFieldSeparator(self):
        return self._varscanFieldSeparator
        
    def getFastqFileName(self):
        return self._fastqFileName
    
    def getRefFastaFileName(self):
        return self._refFastaFileName
    
    def getTaxonName(self):
        return self._taxonName
        
    def createVarscanHit(self, line, currentLineNumber):
        line = line.strip()
        lResults = line.split(self._varscanFieldSeparator)
        iVarscanHit = VarscanHitForGnpSNP()
        iVarscanHit.setAttributes(lResults, currentLineNumber)
        iVarscanHit.formatAlleles2GnpSnp()
        iVarscanHit.manageOccurrence(self._previousVarscanHit)
        self._previousVarscanHit = iVarscanHit
        return iVarscanHit