def main(argv):
snp_data = read_snp_data(open(argv[0]))
out = sys.stdout
for snpline in sorted(snp_data.items()):
snpline = snpline[1]
if snpline.refbase in "ACGUT" and snpline.mutation in "ACGUT":
out.write("%s\n" % snpline.get_gffstring())
else:
# out.write('%s\n' % snpline.get_gffstring())
sys.stderr.write("???: %s\n" % str(snpline))
pass
def main(argv):
snp_data = read_snp_data(open(argv[0]))
outfile = 'ped-0-snps.iit.txt'
if len(argv) >= 2:
outfile = argv[1]
fo = open(outfile, 'w')
for snpline in sorted(snp_data.items()):
snpline = snpline[1]
snp = (snpline.lineid, snpline.seqid, snpline.pos,
snpline.refbase, snpline.mutation)
fo.write('>ped%i %s:%i %c%c\n' % snp)
fo.close()
return None
