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+ − 1 #!/usr/bin/env python
+ − 2 #Dan Blankenberg
+ − 3
+ − 4 """
+ − 5 A wrapper script for running the GenomeAnalysisTK.jar commands.
+ − 6 """
+ − 7
+ − 8 import sys, optparse, os, tempfile, subprocess, shutil
+ − 9 from binascii import unhexlify
+ − 10 from string import Template
+ − 11
+ − 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
+ − 13 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"
+ − 15 CHUNK_SIZE = 2**20 #1mb
+ − 16
+ − 17
+ − 18 def cleanup_before_exit( tmp_dir ):
+ − 19 if tmp_dir and os.path.exists( tmp_dir ):
+ − 20 shutil.rmtree( tmp_dir )
+ − 21
+ − 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 )
+ − 24 if prefix is None:
+ − 25 prefix = DEFAULT_GATK_PREFIX
+ − 26 if target_dir is None:
+ − 27 target_dir = os.getcwd()
+ − 28 gatk_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) )
+ − 29 os.symlink( galaxy_filename, gatk_filename )
+ − 30 return gatk_filename
+ − 31
+ − 32 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
+ − 35 def open_file_from_option( filename, mode = 'rb' ):
+ − 36 if filename:
+ − 37 return open( filename, mode = mode )
+ − 38 return None
+ − 39
+ − 40 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' )
+ − 42 for fname in sorted( os.listdir( dir ) ):
+ − 43 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
+ − 44 html_out.write( '</ul>\n</body>\n</html>\n' )
+ − 45
+ − 46 def index_bam_files( bam_filenames, tmp_dir ):
+ − 47 for bam_filename in bam_filenames:
+ − 48 bam_index_filename = "%s.bai" % bam_filename
+ − 49 if not os.path.exists( bam_index_filename ):
+ − 50 #need to index this bam file
+ − 51 stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name
+ − 52 command = 'samtools index %s %s' % ( bam_filename, bam_index_filename )
+ − 53 proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
+ − 54 return_code = proc.wait()
+ − 55 if return_code:
+ − 56 for line in open( stderr_name ):
+ − 57 print >> sys.stderr, line
+ − 58 os.unlink( stderr_name ) #clean up
+ − 59 cleanup_before_exit( tmp_dir )
+ − 60 raise Exception( "Error indexing BAM file" )
+ − 61 os.unlink( stderr_name ) #clean up
+ − 62
+ − 63 def __main__():
+ − 64 #Parse Command Line
+ − 65 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.' )
+ − 67 parser.add_option( '-o', '--pass_through_options', dest='pass_through_options_encoded', action='append', type="string", help='These options are passed through directly to GATK, with decoding from binascii.unhexlify.' )
+ − 68 parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' )
+ − 69 parser.add_option( '', '--max_jvm_heap', dest='max_jvm_heap', action='store', type="string", default=None, help='If specified, the maximum java virtual machine heap size will be set to the provide value.' )
+ − 70 parser.add_option( '', '--max_jvm_heap_fraction', dest='max_jvm_heap_fraction', action='store', type="int", default=None, help='If specified, the maximum java virtual machine heap size will be set to the provide value as a fraction of total physical memory.' )
+ − 71 parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' )
+ − 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.' )
+ − 73 parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"')
+ − 74 (options, args) = parser.parse_args()
+ − 75
+ − 76 tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' )
+ − 77 if options.pass_through_options:
+ − 78 cmd = ' '.join( options.pass_through_options )
+ − 79 else:
+ − 80 cmd = ''
+ − 81 if options.pass_through_options_encoded:
+ − 82 cmd = '%s %s' % ( cmd, ' '.join( map( unhexlify, options.pass_through_options_encoded ) ) )
+ − 83 if options.max_jvm_heap is not None:
+ − 84 cmd = cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 )
+ − 85 elif options.max_jvm_heap_fraction is not None:
+ − 86 cmd = cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 )
+ − 87 bam_filenames = []
+ − 88 if options.datasets:
+ − 89 for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets:
+ − 90 gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix )
+ − 91 if dataset_arg:
+ − 92 cmd = '%s %s "%s"' % ( cmd, gatk_filetype_argument_substitution( dataset_arg, galaxy_ext ), gatk_filename )
+ − 93 if galaxy_ext == "bam":
+ − 94 bam_filenames.append( gatk_filename )
+ − 95 index_bam_files( bam_filenames, tmp_dir )
+ − 96 #set up stdout and stderr output options
+ − 97 stdout = open_file_from_option( options.stdout, mode = 'wb' )
+ − 98 stderr = open_file_from_option( options.stderr, mode = 'wb' )
+ − 99 #if no stderr file is specified, we'll use our own
+ − 100 if stderr is None:
+ − 101 stderr = tempfile.NamedTemporaryFile( prefix="gatk-stderr-", dir=tmp_dir )
+ − 102
+ − 103 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
+ − 104 return_code = proc.wait()
+ − 105
+ − 106 if return_code:
+ − 107 stderr_target = sys.stderr
+ − 108 else:
+ − 109 stderr_target = sys.stdout
+ − 110 stderr.flush()
+ − 111 stderr.seek(0)
+ − 112 while True:
+ − 113 chunk = stderr.read( CHUNK_SIZE )
+ − 114 if chunk:
+ − 115 stderr_target.write( chunk )
+ − 116 else:
+ − 117 break
+ − 118 stderr.close()
+ − 119 #generate html reports
+ − 120 if options.html_report_from_directory:
+ − 121 for ( html_filename, html_dir ) in options.html_report_from_directory:
+ − 122 html_report_from_directory( open( html_filename, 'wb' ), html_dir )
+ − 123
+ − 124 cleanup_before_exit( tmp_dir )
+ − 125
+ − 126 if __name__=="__main__": __main__()