Пример #1
0
        print 'Pedigree file must contain only case pedigrees for TDT.'
        sys.exit(1)
if TEST == "fbat" and 1 not in pedPhenoDict.values():
        print 'Pedigree file must contain control pedigrees for FBAT.'
        sys.exit(1)



#read feature matrix one line at a time. First two lines have been read above for pedigree ids and member type
for line in fmFile:
	#create new marker object
	#chrM and chrY are not tested
	if line.startswith('chrM') or line.startswith('chr25') or line.startswith('chrY') or line.startswith('chr24'):
		continue	
	elif line.startswith('chrX') or line.startswith('chr23'): 
		thisMarker = ChrXMarker()
	else:  #TODO: more thorough check for validity of data format, like chr numbers??
		thisMarker = AutosomalMarker()
	
	#get vcf columns
 	vcfValues = line.strip().split('\t')

	#assert that all genotype values are numeric #TODO: verify that this assert works
	assert(all(v.isdigit() or v=="NA" for v in vcfValues[1:]))   #1st column is variant id, 2nd onwards are sample genotypes

	
	#set this marker object's sample values 
	thisMarker.markerID = vcfValues[0]
	thisMarker.getSampleGenotypes(vcfValues[1:],pedMemberIndices)
	
	#Note: thought of checking if chrX marker has heterozygous males, but it's not possible since the feature matrix comes in with encoded genotypes. 
Пример #2
0
        print 'Pedigree file must contain only case pedigrees for TDT.'
        sys.exit(1)
if TEST == "fbat" and 1 not in NBPhenoDict.values():
        print 'Pedigree file must contain control pedigrees for FBAT.'
        sys.exit(1)



#read feature matrix one line at a time. First two lines have been read above for pedigree ids and member type
for line in fmFile:
	#create new marker object
	#chrM and chrY are not tested
	if line.startswith('chrM') or line.startswith('chr25') or line.startswith('chrY') or line.startswith('chr24'):
		continue	
	elif line.startswith('chrX') or line.startswith('chr23'): 
		thisMarker = ChrXMarker()
	else:  #TODO: more thorough check for validity of data format, like chr numbers??
		thisMarker = AutosomalMarker()
	
	#get vcf columns
 	vcfValues = line.strip().split('\t')

	#assert that all genotype values are numeric #TODO: verify that this assert works
	assert(all(v.isdigit() or v=="NA" for v in vcfValues[1:]))   #1st column is variant id, 2nd onwards are sample genotypes

	
	#set this marker object's sample values 
	thisMarker.markerID = vcfValues[0]
	thisMarker.getPedGenotypes(vcfValues[1:],sampleIDs,fIDs,mIDs)
	
	#Note: thought of checking if chrX marker has heterozygous males, but it's not possible since the feature matrix comes in with encoded genotypes.