try: #assert that MAF is always positive assert(thisMarker.maf >= 0) except(AssertionError): print 'Marker ',thisMarker.markerID,', MAF=',thisMarker.maf exit(1) #DEBUG # print 'Ref and Alt Frequencies' # print vcfValues[0],thisMarker.maf # raw_input('continue') #get variant distribution if isinstance(thisMarker,ChrXMarker): thisMarker.getVariantDistribution(pedNBGender,pedMemberType) else: thisMarker.getVariantDistribution() #count complete and incomplete case and control trio types and populate corresponding vectors thisMarker.populateTrioTypeCountVectors(pedMemberType,pedPhenoDict,pedNBGender) #concatenate output string and print to output file outputColumns = [thisMarker.markerID,str(thisMarker.maf),str(thisMarker.nVariantType),str(thisMarker.nCompleteInformativeCaseTrio_MaleNB),str(thisMarker.nCompleteInformativeCaseTrio_FemaleNB),str(thisMarker.nCompleteInformativeControlTrio_MaleNB),str(thisMarker.nCompleteInformativeControlTrio_FemaleNB),str(thisMarker.nCompleteNonInformativeCaseTrio),str(thisMarker.nCompleteNonInformativeControlTrio),str(thisMarker.nIncompleteInformativeCaseTrio_MaleNB),str(thisMarker.nIncompleteInformativeCaseTrio_FemaleNB),str(thisMarker.nIncompleteInformativeControlTrio_MaleNB),str(thisMarker.nIncompleteInformativeControlTrio_FemaleNB),str(thisMarker.nIncompleteNonInformativeCaseTrio),str(thisMarker.nIncompleteNonInformativeControlTrio),str(thisMarker.nMIE)] # run appropriate tests based on options selected by the user, add appropriate output columns #**************TDT*************************************************************************** if TEST == "" or TEST == "tdt": #ADDITIVE std. TDT------------------------------------------------------------------- if not MODELS or "a" in MODELS: thisMarker.stdTDT("a") outputColumns.extend([str(thisMarker.chiSq_StdTDT),str(thisMarker.pValue_StdTDT)])
try: #assert that MAF is always positive assert(thisMarker.maf >= 0) except(AssertionError): print 'Marker ',thisMarker.markerID,', MAF=',thisMarker.maf exit(1) #DEBUG # print 'Ref and Alt Frequencies' # print vcfValues[0],thisMarker.maf # raw_input('continue') #get variant distribution if isinstance(thisMarker,ChrXMarker): thisMarker.getVariantDistribution(NBGenderDict) else: thisMarker.getVariantDistribution() #count complete and incomplete case and control trio types and populate corresponding vectors thisMarker.populateTrioTypeCountVectors(NBPhenoDict,NBGenderDict) #concatenate output string and print to output file outputColumns = [thisMarker.markerID,str(thisMarker.maf),str(thisMarker.nVariantType),str(thisMarker.nCompleteInformativeCaseTrio_MaleNB),str(thisMarker.nCompleteInformativeCaseTrio_FemaleNB),str(thisMarker.nCompleteInformativeControlTrio_MaleNB),str(thisMarker.nCompleteInformativeControlTrio_FemaleNB),str(thisMarker.nCompleteNonInformativeCaseTrio),str(thisMarker.nCompleteNonInformativeControlTrio),str(thisMarker.nIncompleteInformativeCaseTrio_MaleNB),str(thisMarker.nIncompleteInformativeCaseTrio_FemaleNB),str(thisMarker.nIncompleteInformativeControlTrio_MaleNB),str(thisMarker.nIncompleteInformativeControlTrio_FemaleNB),str(thisMarker.nIncompleteNonInformativeCaseTrio),str(thisMarker.nIncompleteNonInformativeControlTrio),str(thisMarker.nMIE)] # run appropriate tests based on options selected by the user, add appropriate output columns #**************TDT*************************************************************************** if TEST == "" or TEST == "tdt": #ADDITIVE std. TDT------------------------------------------------------------------- if not MODELS or "a" in MODELS: thisMarker.stdTDT("a") outputColumns.extend([str(thisMarker.chiSq_StdTDT),str(thisMarker.pValue_StdTDT)])