def run(args): # logging.basicConfig(level=logging.DEBUG) dbi = DBI.init(args.bam, "bam") out = IO.fopen(args.output, "w") for i in TableIO.parse(IO.fopen(args.input, "r"), "bed12"): print("QR\t", i, file=out) for j in dbi.query(i, method="bam1", strand=args.strand): if compatible_with_transcript(j, i): print("HT\t{}".format(_translate_to_meta(i, j)), file=out) elif not args.hit: print("OP\t{}".format(j), file=out) print("", file=out)
def run(args): if os.path.isfile(args.bed + ".tbi"): dbi = DBI.init(args.bed, "tabix", cls=BED12) else: dbi = DBI.init(args.bed, "binindex", cls=BED12) out = IO.fopen(args.output, "w") for i in TableIO.parse(IO.fopen(args.input, "r"), "bed12"): print("QR\t", i, file=out) for j in dbi.query(i): if compatible_with_transcript(j, i): print("HT\t{}".format(_translate_to_meta(i, j)), file=out) elif not args.hit: print("OP\t{}".format(j), file=out) print("", file=out)