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)
