#Note: thought of checking if chrX marker has heterozygous males, but it's not possible since the feature matrix comes in with encoded genotypes.
#So all you can check is whether autosomal chrs have any genotypes other than 0/1/2/NA and chrX has any genotypes other that 0/1/NA for males, 0/1/2/NA for females
#for chrX
#TODO: verify that hasValidGenotypes() works
if isinstance(thisMarker,ChrXMarker) and not thisMarker.hasValidGenotypes(pedNBGender,pedMemberType):
print 'Invalid genotype found at ',thisMarker.markerID,'. This marker will not be tested.'
continue
#for autosomal chromosomes
elif not isinstance(thisMarker,ChrXMarker) and not thisMarker.hasValidGenotypes():
print 'Invalid genotype found at ',thisMarker.markerID,'. This marker will not be tested.'
continue
#COMPUTE ALLELE FREQUENCY
#compute regardless of whether 'mi' has been selected or not, because allele frequency will be reported in the output
if isinstance(thisMarker,ChrXMarker):
thisMarker.computeMAF(pedNBGender,pedMemberType)
else:
thisMarker.computeMAF()
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')
#Note: thought of checking if chrX marker has heterozygous males, but it's not possible since the feature matrix comes in with encoded genotypes.
#So all you can check is whether autosomal chrs have any genotypes other than 0/1/2/NA and chrX has any genotypes other that 0/1/NA for males, 0/1/2/NA for females
#for chrX
#TODO: verify that hasValidGenotypes() works
if isinstance(thisMarker,ChrXMarker) and not thisMarker.hasValidGenotypes(NBGenderDict):
print 'Invalid genotype found at ',thisMarker.markerID,'. This marker will not be tested.'
continue
#for autosomal chromosomes
elif not isinstance(thisMarker,ChrXMarker) and not thisMarker.hasValidGenotypes():
print 'Invalid genotype found at ',thisMarker.markerID,'. This marker will not be tested.'
continue
#COMPUTE ALLELE FREQUENCY
#compute regardless of whether 'mi' has been selected or not, because allele frequency will be reported in the output
if isinstance(thisMarker,ChrXMarker):
thisMarker.computeMAF(NBGenderDict)
else:
thisMarker.computeMAF()
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')
