def main():
parser = argparse.ArgumentParser(
"Script to convert from BAM to GTF, for PB alignments")
parser.add_argument(
"--strict",
action="store_true",
default=False,
help=
"Switch. If set, this script will never output multiexonic transcripts \
without a defined strand.")
parser.add_argument("--outfmt", choices=["gtf", "bed12"], default="gtf")
parser.add_argument("bam", type=to_bam, help="Input BAM file")
parser.add_argument("out",
nargs="?",
default=sys.stdout,
type=argparse.FileType("wt"),
help="Optional output file")
args = parser.parse_args()
# M 0 alignment match (can be a sequence match or mismatch)
# I 1 insertion to the reference
# D 2 deletion from the reference
# N 3 skipped region from the reference
# S 4 soft clipping (clipped sequences present in SEQ)
# H 5 hard clipping (clipped sequences NOT present in SEQ)
# P 6 padding (silent deletion from padded reference)
# = 7 sequence match
# X 8 sequence mismatch
name_counter = Counter()
for record in args.bam:
if record.is_unmapped is True:
continue
transcript = Transcript(record,
accept_undefined_multi=(not args.strict))
if name_counter.get(record.query_name):
name = "{}_{}".format(record.query_name,
name_counter.get(record.query_name))
else:
name = record.query_name
if name != transcript.id:
transcript.alias = transcript.id
transcript.id = name
transcript.parent = transcript.attributes[
"gene_id"] = "{0}.gene".format(name)
name_counter.update([record.query_name])
transcript.source = "bam2gtf"
print(transcript.format(args.outfmt), file=args.out)
def launch(args):
"""
Simple launcher script.
:param args: the argparse Namespace
"""
if hasattr(args, "region") and args.region is not None:
try:
args.chrom, args.start, args.end = args.region
except ValueError as exc:
raise ValueError("{0} {1}".format(exc, args.region))
if args.start >= args.end:
raise ValueError("Start greater than end: {0}\t{1}".format(
args.start, args.end))
transcript = None
with GTF(args.gtf) as gtf:
for row in gtf:
if row.chrom != args.chrom:
continue
else:
if row.is_transcript is True:
if transcript is not None and \
transcript.start >= args.start and transcript.end <= args.end:
print(transcript.format("gtf"), file=args.out)
transcript = None
if args.assume_sorted is True and row.start > args.end:
break
transcript = Transcript(row)
else:
transcript.add_exon(row)
if transcript is not None and transcript.start >= args.start and transcript.end <= args.end:
print(transcript.format("gtf"), file=args.out)