def main():
parser = argparse.ArgumentParser(
description="", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input', help="BAM file input")
parser.add_argument('--threads',
type=int,
default=cpu_count(),
help="Thread count")
parser.add_argument('--tempdir',
help="location of temporary directory to use")
parser.add_argument('-o', '--output', help="Output file name")
args = parser.parse_args()
if args.tempdir: args.tempdir = args.tempdir.rstrip('/')
bf = BAMFile(args.input)
seqs = bf.get_header().get_sequence_lengths()
f = tempfile.NamedTemporaryFile(delete=False)
for seq in seqs:
f.write(seq + "\t" + str(seqs[seq]) + "\n")
f.close()
bf.close()
fout = tempfile.NamedTemporaryFile(delete=False)
cmd = 'sort -k 1,1 -k2,2n -k3,3n -S4G --parallel=' + str(args.threads)
if args.tempdir: cmd += ' -T ' + args.tempdir
global ps
ps = Popen(cmd.split(), stdin=PIPE, stdout=fout)
if args.threads > 1:
poo = Pool(processes=args.threads)
for seq in seqs:
if args.threads > 1:
poo.apply_async(do_seq,
args=(seq, args, f.name),
callback=do_output)
else:
res = do_seq(seq, args, f.name)
do_output(res)
if args.threads > 1:
poo.close()
poo.join()
ps.communicate()
fout.close()
of = sys.stdout
if args.output:
if args.output[-3:] == '.gz':
of = gzip.open(args.output, 'w')
else:
of = open(args.output, 'w')
cmd = 'sort -k 1,1 -k2,2n -k3,3n -S4G --parallel=' + str(args.threads)
inf = open(fout.name)
p = Popen(cmd.split(), stdout=PIPE, stdin=inf)
for line in p.stdout:
of.write(line)
p.communicate()
inf.close()
of.close()
os.unlink(f.name)
os.unlink(fout.name)
def main():
parser = argparse.ArgumentParser(description="",formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('input',help="BAM file input")
parser.add_argument('--threads',type=int,default=cpu_count(),help="Thread count")
parser.add_argument('--tempdir',help="location of temporary directory to use")
parser.add_argument('-o','--output',help="Output file name")
args = parser.parse_args()
if args.tempdir: args.tempdir = args.tempdir.rstrip('/')
bf = BAMFile(args.input)
seqs = bf.get_header().get_sequence_lengths()
f = tempfile.NamedTemporaryFile(delete=False)
for seq in seqs:
f.write(seq+"\t"+str(seqs[seq])+"\n")
f.close()
bf.close()
fout = tempfile.NamedTemporaryFile(delete=False)
cmd = 'sort -k 1,1 -k2,2n -k3,3n -S4G --parallel='+str(args.threads)
if args.tempdir: cmd += ' -T '+args.tempdir
global ps
ps = Popen(cmd.split(),stdin=PIPE,stdout=fout)
if args.threads > 1:
poo = Pool(processes=args.threads)
for seq in seqs:
if args.threads > 1:
poo.apply_async(do_seq,args=(seq,args,f.name),callback=do_output)
else:
res = do_seq(seq,args,f.name)
do_output(res)
if args.threads > 1:
poo.close()
poo.join()
ps.communicate()
fout.close()
of = sys.stdout
if args.output:
if args.output[-3:]=='.gz':
of = gzip.open(args.output,'w')
else:
of = open(args.output,'w')
cmd = 'sort -k 1,1 -k2,2n -k3,3n -S4G --parallel='+str(args.threads)
inf = open(fout.name)
p = Popen(cmd.split(),stdout=PIPE,stdin=inf)
for line in p.stdout:
of.write(line)
p.communicate()
inf.close()
of.close()
os.unlink(f.name)
os.unlink(fout.name)
