|
0
|
1 #!/usr/bin/env python
|
|
|
2 """
|
|
|
3 Converts BAM data to sorted SAM data.
|
|
|
4 usage: bam_to_sam.py [options]
|
|
|
5 --input1: SAM file to be converted
|
|
|
6 --output1: output dataset in bam format
|
|
|
7 """
|
|
|
8
|
|
|
9 import optparse, os, sys, subprocess, tempfile, shutil
|
|
|
10 from galaxy import eggs
|
|
|
11 import pkg_resources; pkg_resources.require( "bx-python" )
|
|
|
12 from bx.cookbook import doc_optparse
|
|
|
13 #from galaxy import util
|
|
|
14
|
|
|
15 def stop_err( msg ):
|
|
|
16 sys.stderr.write( '%s\n' % msg )
|
|
|
17 sys.exit()
|
|
|
18
|
|
|
19 def __main__():
|
|
|
20 #Parse Command Line
|
|
|
21 parser = optparse.OptionParser()
|
|
|
22 parser.add_option( '', '--input1', dest='input1', help='The input SAM dataset' )
|
|
|
23 parser.add_option( '', '--output1', dest='output1', help='The output BAM dataset' )
|
|
|
24 parser.add_option( '', '--header', dest='header', action='store_true', default=False, help='Write SAM Header' )
|
|
|
25 ( options, args ) = parser.parse_args()
|
|
|
26
|
|
|
27 # output version # of tool
|
|
|
28 try:
|
|
|
29 tmp = tempfile.NamedTemporaryFile().name
|
|
|
30 tmp_stdout = open( tmp, 'wb' )
|
|
|
31 proc = subprocess.Popen( args='samtools 2>&1', shell=True, stdout=tmp_stdout )
|
|
|
32 tmp_stdout.close()
|
|
|
33 returncode = proc.wait()
|
|
|
34 stdout = None
|
|
|
35 for line in open( tmp_stdout.name, 'rb' ):
|
|
|
36 if line.lower().find( 'version' ) >= 0:
|
|
|
37 stdout = line.strip()
|
|
|
38 break
|
|
|
39 if stdout:
|
|
|
40 sys.stdout.write( 'Samtools %s\n' % stdout )
|
|
|
41 else:
|
|
|
42 raise Exception
|
|
|
43 except:
|
|
|
44 sys.stdout.write( 'Could not determine Samtools version\n' )
|
|
|
45
|
|
|
46 tmp_dir = tempfile.mkdtemp( dir='.' )
|
|
|
47
|
|
|
48 try:
|
|
|
49 # exit if input file empty
|
|
|
50 if os.path.getsize( options.input1 ) == 0:
|
|
|
51 raise Exception, 'Initial BAM file empty'
|
|
|
52 # Sort alignments by leftmost coordinates. File <out.prefix>.bam will be created. This command
|
|
|
53 # may also create temporary files <out.prefix>.%d.bam when the whole alignment cannot be fitted
|
|
|
54 # into memory ( controlled by option -m ).
|
|
|
55 tmp_sorted_aligns_file = tempfile.NamedTemporaryFile( dir=tmp_dir )
|
|
|
56 tmp_sorted_aligns_file_base = tmp_sorted_aligns_file.name
|
|
|
57 tmp_sorted_aligns_file_name = '%s.bam' % tmp_sorted_aligns_file.name
|
|
|
58 tmp_sorted_aligns_file.close()
|
|
|
59 command = 'samtools sort %s %s' % ( options.input1, tmp_sorted_aligns_file_base )
|
|
|
60 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
|
|
|
61 tmp_stderr = open( tmp, 'wb' )
|
|
|
62 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
|
|
|
63 returncode = proc.wait()
|
|
|
64 tmp_stderr.close()
|
|
|
65 # get stderr, allowing for case where it's very large
|
|
|
66 tmp_stderr = open( tmp, 'rb' )
|
|
|
67 stderr = ''
|
|
|
68 buffsize = 1048576
|
|
|
69 try:
|
|
|
70 while True:
|
|
|
71 stderr += tmp_stderr.read( buffsize )
|
|
|
72 if not stderr or len( stderr ) % buffsize != 0:
|
|
|
73 break
|
|
|
74 except OverflowError:
|
|
|
75 pass
|
|
|
76 tmp_stderr.close()
|
|
|
77 if returncode != 0:
|
|
|
78 raise Exception, stderr
|
|
|
79 # exit if sorted BAM file empty
|
|
|
80 if os.path.getsize( tmp_sorted_aligns_file_name) == 0:
|
|
|
81 raise Exception, 'Intermediate sorted BAM file empty'
|
|
|
82 except Exception, e:
|
|
|
83 #clean up temp files
|
|
|
84 if os.path.exists( tmp_dir ):
|
|
|
85 shutil.rmtree( tmp_dir )
|
|
|
86 stop_err( 'Error sorting alignments from (%s), %s' % ( options.input1, str( e ) ) )
|
|
|
87
|
|
|
88
|
|
|
89 try:
|
|
|
90 # Extract all alignments from the input BAM file to SAM format ( since no region is specified, all the alignments will be extracted ).
|
|
|
91 if options.header:
|
|
|
92 view_options = "-h"
|
|
|
93 else:
|
|
|
94 view_options = ""
|
|
|
95 command = 'samtools view %s -o %s %s' % ( view_options, options.output1, tmp_sorted_aligns_file_name )
|
|
|
96 tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name
|
|
|
97 tmp_stderr = open( tmp, 'wb' )
|
|
|
98 proc = subprocess.Popen( args=command, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )
|
|
|
99 returncode = proc.wait()
|
|
|
100 tmp_stderr.close()
|
|
|
101 # get stderr, allowing for case where it's very large
|
|
|
102 tmp_stderr = open( tmp, 'rb' )
|
|
|
103 stderr = ''
|
|
|
104 buffsize = 1048576
|
|
|
105 try:
|
|
|
106 while True:
|
|
|
107 stderr += tmp_stderr.read( buffsize )
|
|
|
108 if not stderr or len( stderr ) % buffsize != 0:
|
|
|
109 break
|
|
|
110 except OverflowError:
|
|
|
111 pass
|
|
|
112 tmp_stderr.close()
|
|
|
113 if returncode != 0:
|
|
|
114 raise Exception, stderr
|
|
|
115 except Exception, e:
|
|
|
116 #clean up temp files
|
|
|
117 if os.path.exists( tmp_dir ):
|
|
|
118 shutil.rmtree( tmp_dir )
|
|
|
119 stop_err( 'Error extracting alignments from (%s), %s' % ( options.input1, str( e ) ) )
|
|
|
120 #clean up temp files
|
|
|
121 if os.path.exists( tmp_dir ):
|
|
|
122 shutil.rmtree( tmp_dir )
|
|
|
123 # check that there are results in the output file
|
|
|
124 if os.path.getsize( options.output1 ) > 0:
|
|
|
125 sys.stdout.write( 'BAM file converted to SAM' )
|
|
|
126 else:
|
|
|
127 stop_err( 'The output file is empty, there may be an error with your input file.' )
|
|
|
128
|
|
|
129 if __name__=="__main__": __main__()
|
