Galaxy - GATK Output

#!/usr/bin/env python #Dan Blankenberg """ A wrapper script for running the GenomeAnalysisTK.jar commands. """ import sys, optparse, os, tempfile, subprocess, shutil from binascii import unhexlify from string import Template 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 GALAXY_EXT_TO_GATK_FILE_TYPE = GALAXY_EXT_TO_GATK_EXT #for now, these are the same, but could be different if needed DEFAULT_GATK_PREFIX = "gatk_file" CHUNK_SIZE = 2**20 #1mb def cleanup_before_exit( tmp_dir ): if tmp_dir and os.path.exists( tmp_dir ): shutil.rmtree( tmp_dir ) def gatk_filename_from_galaxy( galaxy_filename, galaxy_ext, target_dir = None, prefix = None ): suffix = GALAXY_EXT_TO_GATK_EXT.get( galaxy_ext, galaxy_ext ) if prefix is None: prefix = DEFAULT_GATK_PREFIX if target_dir is None: target_dir = os.getcwd() gatk_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) ) os.symlink( galaxy_filename, gatk_filename ) return gatk_filename def gatk_filetype_argument_substitution( argument, galaxy_ext ): return argument % dict( file_type = GALAXY_EXT_TO_GATK_FILE_TYPE.get( galaxy_ext, galaxy_ext ) ) def open_file_from_option( filename, mode = 'rb' ): if filename: return open( filename, mode = mode ) return None def html_report_from_directory( html_out, dir ): html_out.write( '\n\nGalaxy - GATK Output\n\n\n

\n\n\n' ) def index_bam_files( bam_filenames, tmp_dir ): for bam_filename in bam_filenames: bam_index_filename = "%s.bai" % bam_filename if not os.path.exists( bam_index_filename ): #need to index this bam file stderr_name = tempfile.NamedTemporaryFile( prefix = "bam_index_stderr" ).name command = 'samtools index %s %s' % ( bam_filename, bam_index_filename ) proc = subprocess.Popen( args=command, shell=True, stderr=open( stderr_name, 'wb' ) ) return_code = proc.wait() if return_code: for line in open( stderr_name ): print >> sys.stderr, line os.unlink( stderr_name ) #clean up cleanup_before_exit( tmp_dir ) raise Exception( "Error indexing BAM file" ) os.unlink( stderr_name ) #clean up # HACK Ibou : post process def post_process( meta_options, command_line , tempdir) : ''' @param meta_options : list of string, like [ '--otot TATA --titi TUTU' , '-f -L --export', ...] @param command_line : the gatk command line @tempdir : the gatk temp working directory ''' splitted_command_line = [] # remove the double quotes surrounding each command lines parameter for elmt in command_line.split() : if elmt.startswith('"') and elmt.endswith('"'): splitted_command_line.append( elmt[1:-1] ) else : splitted_command_line.append( elmt ) # parse array of string to get all arguments and use opt parse to parse them arguments = [] for sargs in meta_options : arguments.extend(sargs.split()) pparser = optparse.OptionParser() pparser.add_option( '--output-vcf-idx', dest='output_vcf_idx', type="string", help='Index generated by unified genotyper for the vcf file' ) (opts, argss) = pparser.parse_args(arguments) # get the vcf index generated by unified genotyper if opts.output_vcf_idx : if '--out' in splitted_command_line : vcf_name = splitted_command_line[ splitted_command_line.index('--out') + 1 ] index_name = vcf_name + '.idx' shutil.move(index_name, opts.output_vcf_idx) def __main__(): #Parse Command Line parser = optparse.OptionParser() 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.' ) 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.' ) parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' ) 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.' ) 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.' ) 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.' ) 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.' ) parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"') # HACK Ibou : ajouter des parametres de post process parser.add_option( '-P', '--post-process', dest='post_process', action='append', type="string", help='Post process options' ) (options, args) = parser.parse_args() tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' ) if options.pass_through_options: cmd = ' '.join( options.pass_through_options ) else: cmd = '' if options.pass_through_options_encoded: cmd = '%s %s' % ( cmd, ' '.join( map( unhexlify, options.pass_through_options_encoded ) ) ) if options.max_jvm_heap is not None: cmd = cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 ) elif options.max_jvm_heap_fraction is not None: cmd = cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 ) bam_filenames = [] if options.datasets: for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets: gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir = tmp_dir, prefix = prefix ) if dataset_arg: cmd = '%s %s "%s"' % ( cmd, gatk_filetype_argument_substitution( dataset_arg, galaxy_ext ), gatk_filename ) if galaxy_ext == "bam": bam_filenames.append( gatk_filename ) index_bam_files( bam_filenames, tmp_dir ) #set up stdout and stderr output options stdout = open_file_from_option( options.stdout, mode = 'wb' ) stderr = open_file_from_option( options.stderr, mode = 'wb' ) #if no stderr file is specified, we'll use our own if stderr is None: stderr = tempfile.NamedTemporaryFile( prefix="gatk-stderr-", dir=tmp_dir ) proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) return_code = proc.wait() if return_code: stderr_target = sys.stderr else: stderr_target = sys.stdout stderr.flush() stderr.seek(0) while True: chunk = stderr.read( CHUNK_SIZE ) if chunk: stderr_target.write( chunk ) else: break stderr.close() #generate html reports if options.html_report_from_directory: for ( html_filename, html_dir ) in options.html_report_from_directory: html_report_from_directory( open( html_filename, 'wb' ), html_dir ) # HACK Ibou : ajouter un post process if options.post_process : post_process(options.post_process, cmd, tmp_dir) cleanup_before_exit( tmp_dir ) if __name__=="__main__": __main__()