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comparison gatk2_wrapper.py @ 4:f244b8209eb8 draft

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bug fix release
author iuc
date Mon, 25 Aug 2014 17:43:11 -0400
parents 340633249b3d
children 35c00763cb5c
comparison
equal deleted inserted replaced
3:2553f84b8174 4:f244b8209eb8
5 A wrapper script for running the GenomeAnalysisTK.jar commands. 5 A wrapper script for running the GenomeAnalysisTK.jar commands.
6 """ 6 """
7 7
8 import sys, optparse, os, tempfile, subprocess, shutil 8 import sys, optparse, os, tempfile, subprocess, shutil
9 from binascii import unhexlify 9 from binascii import unhexlify
10 from string import Template
11 10
12 GALAXY_EXT_TO_GATK_EXT = { 'gatk_interval':'intervals', 'bam_index':'bam.bai', 'gatk_dbsnp':'dbSNP', 'picard_interval_list':'interval_list' } #items not listed here will use the galaxy extension as-is 11 GALAXY_EXT_TO_GATK_EXT = { 'gatk_interval':'intervals', 'bam_index':'bam.bai', 'gatk_dbsnp':'dbSNP', 'picard_interval_list':'interval_list' } #items not listed here will use the galaxy extension as-is
13 GALAXY_EXT_TO_GATK_FILE_TYPE = GALAXY_EXT_TO_GATK_EXT #for now, these are the same, but could be different if needed 12 GALAXY_EXT_TO_GATK_FILE_TYPE = GALAXY_EXT_TO_GATK_EXT #for now, these are the same, but could be different if needed
14 DEFAULT_GATK_PREFIX = "gatk_file" 13 DEFAULT_GATK_PREFIX = "gatk_file"
15 CHUNK_SIZE = 2**20 #1mb 14 CHUNK_SIZE = 2**20 #1mb
17 16
18 def cleanup_before_exit( tmp_dir ): 17 def cleanup_before_exit( tmp_dir ):
19 if tmp_dir and os.path.exists( tmp_dir ): 18 if tmp_dir and os.path.exists( tmp_dir ):
20 shutil.rmtree( tmp_dir ) 19 shutil.rmtree( tmp_dir )
21 20
21
22 def gatk_filename_from_galaxy( galaxy_filename, galaxy_ext, target_dir = None, prefix = None ): 22 def gatk_filename_from_galaxy( galaxy_filename, galaxy_ext, target_dir = None, prefix = None ):
23 suffix = GALAXY_EXT_TO_GATK_EXT.get( galaxy_ext, galaxy_ext ) 23 suffix = GALAXY_EXT_TO_GATK_EXT.get( galaxy_ext, galaxy_ext )
24 if prefix is None: 24 if prefix is None:
25 prefix = DEFAULT_GATK_PREFIX 25 prefix = DEFAULT_GATK_PREFIX
26 if target_dir is None: 26 if target_dir is None:
27 target_dir = os.getcwd() 27 target_dir = os.getcwd()
28 gatk_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) ) 28 gatk_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) )
29 os.symlink( galaxy_filename, gatk_filename ) 29 os.symlink( galaxy_filename, gatk_filename )
30 return gatk_filename 30 return gatk_filename
31 31
32
32 def gatk_filetype_argument_substitution( argument, galaxy_ext ): 33 def gatk_filetype_argument_substitution( argument, galaxy_ext ):
33 return argument % dict( file_type = GALAXY_EXT_TO_GATK_FILE_TYPE.get( galaxy_ext, galaxy_ext ) ) 34 return argument % dict( file_type = GALAXY_EXT_TO_GATK_FILE_TYPE.get( galaxy_ext, galaxy_ext ) )
35
34 36
35 def open_file_from_option( filename, mode = 'rb' ): 37 def open_file_from_option( filename, mode = 'rb' ):
36 if filename: 38 if filename:
37 return open( filename, mode = mode ) 39 return open( filename, mode = mode )
38 return None 40 return None
41
39 42
40 def html_report_from_directory( html_out, dir ): 43 def html_report_from_directory( html_out, dir ):
41 html_out.write( '<html>\n<head>\n<title>Galaxy - GATK Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' ) 44 html_out.write( '<html>\n<head>\n<title>Galaxy - GATK Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
42 for fname in sorted( os.listdir( dir ) ): 45 for fname in sorted( os.listdir( dir ) ):
43 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) ) 46 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
44 html_out.write( '</ul>\n</body>\n</html>\n' ) 47 html_out.write( '</ul>\n</body>\n</html>\n' )
45 48
46 def index_bam_files( bam_filenames, tmp_dir ): 49
50 def index_bam_files( bam_filenames ):
47 for bam_filename in bam_filenames: 51 for bam_filename in bam_filenames:
48 bam_index_filename = "%s.bai" % bam_filename 52 bam_index_filename = "%s.bai" % bam_filename
49 if not os.path.exists( bam_index_filename ): 53 if not os.path.exists( bam_index_filename ):
50 #need to index this bam file 54 #need to index this bam file
51 stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name 55 stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
52 command = 'samtools index %s %s' % ( bam_filename, bam_index_filename ) 56 command = 'samtools index %s %s' % ( bam_filename, bam_index_filename )
53 proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) ) 57 try:
54 return_code = proc.wait() 58 subprocess.check_call( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
55 if return_code: 59 except:
56 for line in open( stderr_name ): 60 for line in open( stderr_name ):
57 print >> sys.stderr, line 61 print >> sys.stderr, line
58 os.unlink( stderr_name ) #clean up
59 cleanup_before_exit( tmp_dir )
60 raise Exception( "Error indexing BAM file" ) 62 raise Exception( "Error indexing BAM file" )
61 os.unlink( stderr_name ) #clean up 63 finally:
64 os.unlink( stderr_name )
62 65
63 def __main__(): 66 def __main__():
64 #Parse Command Line 67 #Parse Command Line
65 parser = optparse.OptionParser() 68 parser = optparse.OptionParser()
66 parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to GATK, without any modification.' ) 69 parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to GATK, without any modification.' )
72 parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' ) 75 parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' )
73 parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"') 76 parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"')
74 parser.add_option( '-e', '--phone_home', dest='phone_home', action='store', type="string", default='STANDARD', help='What kind of GATK run report should we generate(NO_ET|STANDARD|STDOUT)' ) 77 parser.add_option( '-e', '--phone_home', dest='phone_home', action='store', type="string", default='STANDARD', help='What kind of GATK run report should we generate(NO_ET|STANDARD|STDOUT)' )
75 parser.add_option( '-K', '--gatk_key', dest='gatk_key', action='store', type="string", default=None, help='What kind of GATK run report should we generate(NO_ET|STANDARD|STDOUT)' ) 78 parser.add_option( '-K', '--gatk_key', dest='gatk_key', action='store', type="string", default=None, help='What kind of GATK run report should we generate(NO_ET|STANDARD|STDOUT)' )
76 (options, args) = parser.parse_args() 79 (options, args) = parser.parse_args()
77 80
78 tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' )
79 if options.pass_through_options: 81 if options.pass_through_options:
80 cmd = ' '.join( options.pass_through_options ) 82 cmd = ' '.join( options.pass_through_options )
81 else: 83 else:
82 cmd = '' 84 cmd = ''
83 if options.pass_through_options_encoded: 85 if options.pass_through_options_encoded:
85 if options.max_jvm_heap is not None: 87 if options.max_jvm_heap is not None:
86 cmd = cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 ) 88 cmd = cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 )
87 elif options.max_jvm_heap_fraction is not None: 89 elif options.max_jvm_heap_fraction is not None:
88 cmd = cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 ) 90 cmd = cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 )
89 bam_filenames = [] 91 bam_filenames = []
90 if options.datasets: 92 tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' )
91 for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets: 93 try:
92 gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix ) 94 if options.datasets:
93 if dataset_arg: 95 for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets:
94 cmd = '%s %s "%s"' % ( cmd, gatk_filetype_argument_substitution( dataset_arg, galaxy_ext ), gatk_filename ) 96 gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix )
95 if galaxy_ext == "bam": 97 if dataset_arg:
96 bam_filenames.append( gatk_filename ) 98 cmd = '%s %s "%s"' % ( cmd, gatk_filetype_argument_substitution( dataset_arg, galaxy_ext ), gatk_filename )
97 index_bam_files( bam_filenames, tmp_dir ) 99 if galaxy_ext == "bam":
98 #set up stdout and stderr output options 100 bam_filenames.append( gatk_filename )
99 stdout = open_file_from_option( options.stdout, mode = 'wb' ) 101 if galaxy_ext == 'fasta':
100 stderr = open_file_from_option( options.stderr, mode = 'wb' ) 102 subprocess.check_call( 'samtools faidx "%s"' % gatk_filename, shell=True )
101 #if no stderr file is specified, we'll use our own 103 subprocess.check_call( 'java -jar %s R=%s O=%s QUIET=true' % ( os.path.join(os.environ['JAVA_JAR_PATH'], 'CreateSequenceDictionary.jar'), gatk_filename, os.path.splitext(gatk_filename)[0] + '.dict' ), shell=True )
102 if stderr is None: 104 index_bam_files( bam_filenames )
103 stderr = tempfile.NamedTemporaryFile( prefix="gatk-stderr-", dir=tmp_dir ) 105 #set up stdout and stderr output options
104 106 stdout = open_file_from_option( options.stdout, mode = 'wb' )
105 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) 107 stderr = open_file_from_option( options.stderr, mode = 'wb' )
106 return_code = proc.wait() 108 #if no stderr file is specified, we'll use our own
107 109 if stderr is None:
108 if return_code: 110 stderr = tempfile.NamedTemporaryFile( prefix="gatk-stderr-", dir=tmp_dir )
109 stderr_target = sys.stderr 111
110 else: 112 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
111 stderr_target = sys.stdout 113 return_code = proc.wait()
112 stderr.flush() 114
113 stderr.seek(0) 115 if return_code:
114 while True: 116 stderr_target = sys.stderr
115 chunk = stderr.read( CHUNK_SIZE )
116 if chunk:
117 stderr_target.write( chunk )
118 else: 117 else:
119 break 118 stderr_target = sys.stdout
120 stderr.close() 119 stderr.flush()
120 stderr.seek(0)
121 while True:
122 chunk = stderr.read( CHUNK_SIZE )
123 if chunk:
124 stderr_target.write( chunk )
125 else:
126 break
127 stderr.close()
128 finally:
129 cleanup_before_exit( tmp_dir )
130
121 #generate html reports 131 #generate html reports
122 if options.html_report_from_directory: 132 if options.html_report_from_directory:
123 for ( html_filename, html_dir ) in options.html_report_from_directory: 133 for ( html_filename, html_dir ) in options.html_report_from_directory:
124 html_report_from_directory( open( html_filename, 'wb' ), html_dir ) 134 html_report_from_directory( open( html_filename, 'wb' ), html_dir )
125
126 cleanup_before_exit( tmp_dir )
127 135
128 if __name__=="__main__": __main__() 136
137 if __name__ == "__main__":
138 __main__()