Mercurial > repos > xuebing > sharplabtool
comparison tools/samtools/bam_to_sam.py @ 0:9071e359b9a3
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author | xuebing |
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date | Fri, 09 Mar 2012 19:37:19 -0500 |
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-1:000000000000 | 0:9071e359b9a3 |
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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() | |
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__() |