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)])
