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