def dostream(stream):
reader = SamLocusStream(stream)
while True:
locus = reader.read_locus()
if not locus: break
print locus[0].chr + "\t" + str(locus[0].start - 1) + "\t" + str(
locus[0].end)
def dopart(stream):
reader = SamLocusStream(stream)
v = []
while True:
locus = reader.read_locus()
if not locus: break
v.append(locus[0].chr+"\t"+str(locus[0].start-1)+"\t"+str(locus[0].end))
return v
def dopart(stream):
reader = SamLocusStream(stream)
v = []
while True:
locus = reader.read_locus()
if not locus: break
v.append(locus[0].chr + "\t" + str(locus[0].start - 1) + "\t" +
str(locus[0].end))
return v
def main():
parser = argparse.ArgumentParser()
parser.add_argument('--min_intron',type=int,default=68)
parser.add_argument('--min_depth',type=int,default=1)
parser.add_argument('-v','--verbose',action='store_true')
parser.add_argument('input',help="BAM file or stream sam input with header with -")
args = parser.parse_args()
if args.input == '-': inf = sys.stdin
else:
cmd = "samtools view -h "+args.input
p = Popen(cmd.split(),stdout=PIPE,bufsize=1)
inf = p.stdout
s = SamLocusStream(inf)
#s.junctions_only = False
while True:
locus = s.read_locus()
if not locus: break
#print locus[0].get_range_string()+"\t"+str(len(locus[1]))
process_locus(locus[1],args)
if args.input != '-': p.communicate()
def dostream(stream):
reader = SamLocusStream(stream)
while True:
locus = reader.read_locus()
if not locus: break
print locus[0].chr+"\t"+str(locus[0].start-1)+"\t"+str(locus[0].end)
