Mercurial > repos > devteam > samtools_slice_bam

comparison samtools_slice_bam.py @ 0:68ba55e96489 draft

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author devteam
date Mon, 26 Aug 2013 14:25:12 -0400
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-1:000000000000 0:68ba55e96489
1 #!/usr/bin/env python
2 #Dan Blankenberg
3
4 """
5 A wrapper script for slicing a BAM file by provided BED file using SAMTools.
6 %prog input_filename.sam output_filename.bam
7 """
8 #TODO: Confirm that the sort is necessary e.g. if input regions are out of order
9
10
11 import sys, optparse, os, tempfile, subprocess, shutil
12
13 CHUNK_SIZE = 2**20 #1mb
14
15 def cleanup_before_exit( tmp_dir ):
16 if tmp_dir and os.path.exists( tmp_dir ):
17 shutil.rmtree( tmp_dir )
18
19 def __main__():
20 #Parse Command Line
21 parser = optparse.OptionParser()
22 (options, args) = parser.parse_args()
23
24 assert len( args ) == 4, "Invalid command line: samtools_slice_bam.py input.bam input.bam.bai input.interval output.bam"
25 input_bam_filename, input_index_filename, input_interval_filename, output_bam_filename = args
26
27 tmp_dir = tempfile.mkdtemp( prefix='tmp-samtools_slice_bam-' )
28
29 tmp_input_bam_filename = os.path.join( tmp_dir, 'input_bam.bam' )
30 os.symlink( input_bam_filename, tmp_input_bam_filename )
31 os.symlink( input_index_filename, "%s.bai" % tmp_input_bam_filename )
32
33 #Slice BAM
34 unsorted_bam_filename = os.path.join( tmp_dir, 'unsorted.bam' )
35 unsorted_stderr_filename = os.path.join( tmp_dir, 'unsorted.stderr' )
36 cmd = 'samtools view -b -L "%s" "%s" > "%s"' % ( input_interval_filename, tmp_input_bam_filename, unsorted_bam_filename )
37 proc = subprocess.Popen( args=cmd, stderr=open( unsorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
38 return_code = proc.wait()
39 if return_code:
40 stderr_target = sys.stderr
41 else:
42 stderr_target = sys.stdout
43 stderr = open( unsorted_stderr_filename )
44 while True:
45 chunk = stderr.read( CHUNK_SIZE )
46 if chunk:
47 stderr_target.write( chunk )
48 else:
49 break
50 stderr.close()
51
52 #sort sam, so indexing will not fail
53 #TODO: confirm if sorting is necessary (is original BAM order maintained, or does the output follow the order of input intervals?)
54 sorted_stderr_filename = os.path.join( tmp_dir, 'sorted.stderr' )
55 sorting_prefix = os.path.join( tmp_dir, 'sorted_bam' )
56 cmd = 'samtools sort -o "%s" "%s" > "%s"' % ( unsorted_bam_filename, sorting_prefix, output_bam_filename )
57 proc = subprocess.Popen( args=cmd, stderr=open( sorted_stderr_filename, 'wb' ), shell=True, cwd=tmp_dir )
58 return_code = proc.wait()
59
60 if return_code:
61 stderr_target = sys.stderr
62 else:
63 stderr_target = sys.stdout
64 stderr = open( sorted_stderr_filename )
65 while True:
66 chunk = stderr.read( CHUNK_SIZE )
67 if chunk:
68 stderr_target.write( chunk )
69 else:
70 break
71 stderr.close()
72
73 cleanup_before_exit( tmp_dir )
74
75 if __name__=="__main__": __main__()