0
+ − 1 #!/usr/bin/env python
+ − 2 #Dan Blankenberg
+ − 3
+ − 4 """
+ − 5 A wrapper script for running the Picard SamToFastq command. Allows parsing read groups into separate files.
+ − 6 """
+ − 7
+ − 8 import sys, optparse, os, tempfile, subprocess, shutil
+ − 9
+ − 10 CHUNK_SIZE = 2**20 #1mb
+ − 11
+ − 12
+ − 13 def cleanup_before_exit( tmp_dir ):
+ − 14 if tmp_dir and os.path.exists( tmp_dir ):
+ − 15 shutil.rmtree( tmp_dir )
+ − 16
+ − 17 def open_file_from_option( filename, mode = 'rb' ):
+ − 18 if filename:
+ − 19 return open( filename, mode = mode )
+ − 20 return None
+ − 21
+ − 22 def __main__():
+ − 23 #Parse Command Line
+ − 24 parser = optparse.OptionParser()
+ − 25 parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to PICARD, without any modification.' )
+ − 26 parser.add_option( '-1', '--read_group_file_1', dest='read_group_file_1', action='store', type="string", default=None, help='Read Group 1 output file, when using multiple readgroups' )
+ − 27 parser.add_option( '-2', '--read_group_file_2', dest='read_group_file_2', action='store', type="string", default=None, help='Read Group 2 output file, when using multiple readgroups and paired end' )
+ − 28 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.' )
+ − 29 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.' )
+ − 30 parser.add_option( '-n', '--new_files_path', dest='new_files_path', action='store', type="string", default=None, help='new_files_path')
+ − 31 parser.add_option( '-i', '--file_id_1', dest='file_id_1', action='store', type="string", default=None, help='file_id_1')
+ − 32 parser.add_option( '-f', '--file_id_2', dest='file_id_2', action='store', type="string", default=None, help='file_id_2')
+ − 33 (options, args) = parser.parse_args()
+ − 34
+ − 35 tmp_dir = tempfile.mkdtemp( prefix='tmp-picard-' )
+ − 36 if options.pass_through_options:
+ − 37 cmd = ' '.join( options.pass_through_options )
+ − 38 else:
+ − 39 cmd = ''
+ − 40 if options.new_files_path is not None:
+ − 41 print 'Creating FASTQ files by Read Group'
+ − 42 assert None not in [ options.read_group_file_1, options.new_files_path, options.file_id_1 ], 'When using read group aware, you need to specify --read_group_file_1, --read_group_file_2 (when paired end), --new_files_path, and --file_id'
+ − 43 cmd = '%s OUTPUT_DIR="%s"' % ( cmd, tmp_dir)
+ − 44 #set up stdout and stderr output options
+ − 45 stdout = open_file_from_option( options.stdout, mode = 'wb' )
+ − 46 if stdout is None:
+ − 47 stdout = sys.stdout
+ − 48 stderr = open_file_from_option( options.stderr, mode = 'wb' )
+ − 49 #if no stderr file is specified, we'll use our own
+ − 50 if stderr is None:
+ − 51 stderr = tempfile.NamedTemporaryFile( prefix="picard-stderr-", dir=tmp_dir )
+ − 52
+ − 53 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
+ − 54 return_code = proc.wait()
+ − 55
+ − 56 if return_code:
+ − 57 stderr_target = sys.stderr
+ − 58 else:
+ − 59 stderr_target = sys.stdout
+ − 60 stderr.flush()
+ − 61 stderr.seek(0)
+ − 62 while True:
+ − 63 chunk = stderr.read( CHUNK_SIZE )
+ − 64 if chunk:
+ − 65 stderr_target.write( chunk )
+ − 66 else:
+ − 67 break
+ − 68 stderr.close()
+ − 69 #if rg aware, put files where they belong
+ − 70 if options.new_files_path is not None:
+ − 71 fastq_1_name = options.read_group_file_1
+ − 72 fastq_2_name = options.read_group_file_2
+ − 73 file_id_1 = options.file_id_1
+ − 74 file_id_2 = options.file_id_2
+ − 75 if file_id_2 is None:
+ − 76 file_id_2 = file_id_1
+ − 77 for filename in sorted( os.listdir( tmp_dir ) ):
+ − 78 if filename.endswith( '_1.fastq' ):
+ − 79 if fastq_1_name:
+ − 80 shutil.move( os.path.join( tmp_dir, filename ), fastq_1_name )
+ − 81 fastq_1_name = None
+ − 82 else:
+ − 83 shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastqsanger' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) )
+ − 84 elif filename.endswith( '_2.fastq' ):
+ − 85 if fastq_2_name:
+ − 86 shutil.move( os.path.join( tmp_dir, filename ), fastq_2_name )
+ − 87 fastq_2_name = None
+ − 88 else:
+ − 89 shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastqsanger' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) )
+ − 90
+ − 91 cleanup_before_exit( tmp_dir )
+ − 92
+ − 93 if __name__=="__main__": __main__()
