Mercurial > repos > iuc > gatk2
diff gatk2_wrapper.py @ 4:f244b8209eb8 draft
bug fix release
| author | iuc |
|---|---|
| date | Mon, 25 Aug 2014 17:43:11 -0400 |
| parents | 340633249b3d |
| children | 35c00763cb5c |
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--- a/gatk2_wrapper.py Wed Feb 19 04:39:38 2014 -0500 +++ b/gatk2_wrapper.py Mon Aug 25 17:43:11 2014 -0400 @@ -7,7 +7,6 @@ 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 @@ -19,6 +18,7 @@ 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: @@ -29,36 +29,39 @@ 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( '<html>\n<head>\n<title>Galaxy - GATK Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' ) for fname in sorted( os.listdir( dir ) ): html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) ) html_out.write( '</ul>\n</body>\n</html>\n' ) -def index_bam_files( bam_filenames, tmp_dir ): + +def index_bam_files( bam_filenames ): 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: + try: + subprocess.check_call( args=command, shell=True, stderr=open( stderr_name, 'wb' ) ) + except: 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 + finally: + os.unlink( stderr_name ) def __main__(): #Parse Command Line @@ -74,8 +77,7 @@ 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)' ) 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)' ) (options, args) = parser.parse_args() - - tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' ) + if options.pass_through_options: cmd = ' '.join( options.pass_through_options ) else: @@ -87,42 +89,50 @@ 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 ) + tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' ) + try: + 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 ) + if galaxy_ext == 'fasta': + subprocess.check_call( 'samtools faidx "%s"' % gatk_filename, shell=True ) + 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 ) + index_bam_files( bam_filenames ) + #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: - break - stderr.close() + 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() + finally: + cleanup_before_exit( tmp_dir ) + #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 ) - - cleanup_before_exit( tmp_dir ) + -if __name__=="__main__": __main__() +if __name__ == "__main__": + __main__()