annotate smart_toolShed/commons/core/parsing/VarscanHit_WithTag.py @ 0:e0f8dcca02ed

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

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from commons.core.parsing.VarscanHit import VarscanHit

class VarscanHit_WithTag(VarscanHit):
    
    def __init__(self, tag = "", chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""):
        self._tag = tag
        VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue)
        
    def __eq__(self, o):
        if self._tag == o._tag: 
            return VarscanHit.__eq__(self, o)
        return False
    
    def setTag(self, tag):
        self._tag = tag
        
    def getTag(self):
        return self._tag
    
    def getHeader(self):
        return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tTag\n"
    
    def getVarscanLine(self):
        return "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (self.getChrom(), self.getPosition(), self.getRef(), self.getVar(), self.getReadsRef(), self.getReadsVar(), self.getVarFreq(), self.getStrandsRef(), self.getStrandsVar(),  self.getQualRef(), self.getQualVar(), self.getPValue(), self.getTag())
    
    def setAttributes(self, lResults, iCurrentLineNumber):
        VarscanHit.setAttributes(self, lResults, iCurrentLineNumber)
        if lResults[12] != '':
            self.setTag(lResults[12])
            
    def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
        varscanString = varscanString.rstrip()
        lvarscanStringItem = varscanString.split(fieldSeparator)
        if len(lvarscanStringItem)<13:
            for i in range(len(lvarscanStringItem), 13):
                lvarscanStringItem.append ("")
        self.setAttributes(lvarscanStringItem, iCurrentLineNumber)