def main():
parser = OptionParser(usage=usage)
(options, args) = parser.parse_args()
list_of_autosomes = range(1,23)
for autosome in list_of_autosomes:
# read tag SNP file
tag_snp_file = open("Results/tags_chr" + str(autosome) + ".txt")
tag_snp_file.next() # discard header
#print('Processing tag SNP file...')
del_snp_pairs, snp_positions = [], []
for line in tag_snp_file:
del_snp_pairs.append(DeletionTAGSNPPair(line))
snp_positions.append(del_snp_pairs[-1].snp_pos)
#print('DONE processing tag SNP file...')
# read VCF file
#print('Processing VCF file...')
snp_reader = SNPReader(1, max_major_af = .96)
snp_reader.readRawList(snp_positions)
#print('DONE Processing VCF file...')
# Postprocess every tag SNP-deletion pair
for del_snp_pair in del_snp_pairs:
for snp in snp_reader.snps:
if del_snp_pair.snp_pos == snp.position:
del_snp_pair.addReferenceAlternativeAllele(snp.vcf_record.REF, snp.vcf_record.ALT[0])
del_snp_pair.update()
del_snp_pair.print()
def main():
parser = OptionParser(usage=usage)
parser.add_option("-a", action="store", dest="max_major_af", default=.96, type=float,
help="Max. major allele frequency for a deletion and a snp to be considered. (Default = .96)")
parser.add_option("-d", action="store", dest="distance_threshold", default=1000000, type=int,
help="Max. distance between SNP and deletion for the pair to be considered. (Default = 10^6)")
(options, args) = parser.parse_args()
if (len(args)!=1):
parser.print_help()
return 1
chromosome = int(args[0])
deletion_reader = DeletionReader(max_major_af = options.max_major_af)
# Read in the relevant data
deletion_reader.read(chromosome)
snp_reader = SNPReader(chromosome, max_major_af = options.max_major_af)
snp_reader.read()
print('# of SNPs now: ', len(snp_reader.snps))
# walk through all SNPs:
for snp in snp_reader.snps:
# walk through all deletions
for deletion in deletion_reader.deletions:
distance_snp_deletion = deletion.minimumDistanceTo(snp.position)
if distance_snp_deletion > options.distance_threshold:
continue
table = Table2x2(snp.haplotypes, deletion.haplotypes)
# output relevant data:
snp.store()
deletion.store()
print(distance_snp_deletion, '\t', end = '')
table.store()
print(table.R(), '\t', table.FishersExactTest())
