/tools/gatk/gatk_wrapper.py
Python | 126 lines | 103 code | 15 blank | 8 comment | 22 complexity | 90f5a44f1e756b8e3020fc40fb22ed76 MD5 | raw file
1#!/usr/bin/env python 2#Dan Blankenberg 3 4""" 5A wrapper script for running the GenomeAnalysisTK.jar commands. 6""" 7 8import sys, optparse, os, tempfile, subprocess, shutil 9from binascii import unhexlify 10from string import Template 11 12GALAXY_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 13GALAXY_EXT_TO_GATK_FILE_TYPE = GALAXY_EXT_TO_GATK_EXT #for now, these are the same, but could be different if needed 14DEFAULT_GATK_PREFIX = "gatk_file" 15CHUNK_SIZE = 2**20 #1mb 16 17 18def cleanup_before_exit( tmp_dir ): 19 if tmp_dir and os.path.exists( tmp_dir ): 20 shutil.rmtree( tmp_dir ) 21 22def 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 32def 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 35def open_file_from_option( filename, mode = 'rb' ): 36 if filename: 37 return open( filename, mode = mode ) 38 return None 39 40def 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 46def 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 63def __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 126if __name__=="__main__": __main__()