Mercurial > repos > greg > bam_to_scidx

comparison bam_to_scidx.py @ 0:962b0366a980 draft

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author greg
date Tue, 24 Nov 2015 08:13:56 -0500
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-1:000000000000 0:962b0366a980
1 """
2 bam_to_scidx.py
3
4 Input: BAM file
5 Output: Converted scidx file
6 """
7 import optparse
8 import os
9 import shutil
10 import subprocess
11 import sys
12 import tempfile
13
14 BUFF_SIZE = 1048576
15
16
17 def get_stderr_exception(tmp_err, tmp_stderr):
18 """
19 Return a stderr string of reasonable size.
20 """
21 tmp_stderr.close()
22 # Get stderr, allowing for case where it's very large.
23 tmp_stderr = open(tmp_err, 'rb')
24 stderr_str = ''
25 buffsize = BUFF_SIZE
26 try:
27 while True:
28 stderr_str += tmp_stderr.read(buffsize)
29 if not stderr_str or len(stderr_str) % buffsize != 0:
30 break
31 except OverflowError:
32 pass
33 tmp_stderr.close()
34 return stderr_str
35
36
37 def stop_err(msg):
38 sys.stderr.write(msg)
39 sys.exit(1)
40
41
42 parser = optparse.OptionParser()
43 parser.add_option('-j', '--jar_file', dest='jar_file', type='string', help='BAMtoIDX.jar')
44 parser.add_option('-b', '--input_bam', dest='input_bam', type='string', help='Input dataset in BAM format')
45 parser.add_option('-i', '--input_bai', dest='input_bai', type='string', help='Input dataset index')
46 parser.add_option('-r', '--read', dest='read', type='int', default=0, help='Reads.')
47 parser.add_option('-o', '--output', dest='output', type='string', help='Output dataset in scidx format')
48 options, args = parser.parse_args()
49
50 tmp_dir = tempfile.mkdtemp(prefix='tmp-scidx-')
51 tmp_out = tempfile.NamedTemporaryFile().name
52 tmp_stdout = open(tmp_out, 'wb')
53 tmp_err = tempfile.NamedTemporaryFile().name
54 tmp_stderr = open(tmp_err, 'wb')
55
56 # Link input BAM file and associated index file into the working directory.
57 input_data_file_name = "input.bam"
58 os.link(options.input_bam, os.path.join(tmp_dir, input_data_file_name))
59 os.link(options.input_bai, os.path.join(tmp_dir, "%s.bai" % input_data_file_name))
60
61 cmd = "java -jar %s -b %s -s %d -o %s" % (options.jar_file, input_data_file_name, options.read, options.output)
62 proc = subprocess.Popen(args=cmd, stdout=tmp_stdout, stderr=tmp_stderr, shell=True, cwd=tmp_dir)
63 return_code = proc.wait()
64 if return_code != 0:
65 error_message = get_stderr_exception(tmp_err, tmp_stderr)
66 stop_err(error_message)
67
68 if tmp_dir and os.path.exists(tmp_dir):
69 shutil.rmtree(tmp_dir)