def compilevcf(args): """ %prog compilevcf dir Compile vcf outputs into lists. """ from jcvi.variation.str import LobSTRvcf p = OptionParser(compilevcf.__doc__) opts, args = p.parse_args(args) if len(args) != 1: sys.exit(not p.print_help()) folder, = args vcf_files = iglob(folder, "*.vcf,*.vcf.gz") for vcf_file in vcf_files: try: p = LobSTRvcf(columnidsfile=None) p.parse(vcf_file, filtered=False) res = p.items() if res: k, v = res[0] res = v.replace(',', '/') else: res = "-1/-1" num = op.basename(vcf_file).split(".")[0] print num, res except (TypeError, AttributeError) as e: p = TREDPARSEvcf(vcf_file) continue