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1 #!/usr/bin/env python
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2 #Dan Blankenberg
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3
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4 """
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5 A wrapper script for running the Picard SamToFastq command. Allows parsing read groups into separate files.
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6 """
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7
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8 import sys, optparse, os, tempfile, subprocess, shutil
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9
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10 CHUNK_SIZE = 2**20 #1mb
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11
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12
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13 def cleanup_before_exit( tmp_dir ):
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14 if tmp_dir and os.path.exists( tmp_dir ):
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15 shutil.rmtree( tmp_dir )
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16
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17 def open_file_from_option( filename, mode = 'rb' ):
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18 if filename:
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19 return open( filename, mode = mode )
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20 return None
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21
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22 def __main__():
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23 #Parse Command Line
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24 parser = optparse.OptionParser()
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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.' )
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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' )
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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' )
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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.' )
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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.' )
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30 parser.add_option( '-n', '--new_files_path', dest='new_files_path', action='store', type="string", default=None, help='new_files_path')
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31 parser.add_option( '-i', '--file_id_1', dest='file_id_1', action='store', type="string", default=None, help='file_id_1')
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32 parser.add_option( '-f', '--file_id_2', dest='file_id_2', action='store', type="string", default=None, help='file_id_2')
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33 (options, args) = parser.parse_args()
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34
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35 tmp_dir = tempfile.mkdtemp( prefix='tmp-picard-' )
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36 if options.pass_through_options:
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37 cmd = ' '.join( options.pass_through_options )
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38 else:
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39 cmd = ''
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40 if options.new_files_path is not None:
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41 print 'Creating FASTQ files by Read Group'
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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'
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43 cmd = '%s OUTPUT_DIR="%s"' % ( cmd, tmp_dir)
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44 #set up stdout and stderr output options
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45 stdout = open_file_from_option( options.stdout, mode = 'wb' )
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46 if stdout is None:
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47 stdout = sys.stdout
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48 stderr = open_file_from_option( options.stderr, mode = 'wb' )
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49 #if no stderr file is specified, we'll use our own
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50 if stderr is None:
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51 stderr = tempfile.NamedTemporaryFile( prefix="picard-stderr-", dir=tmp_dir )
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52
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53 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
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54 return_code = proc.wait()
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55
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56 if return_code:
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57 stderr_target = sys.stderr
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58 else:
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59 stderr_target = sys.stdout
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60 stderr.flush()
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61 stderr.seek(0)
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62 while True:
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63 chunk = stderr.read( CHUNK_SIZE )
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64 if chunk:
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65 stderr_target.write( chunk )
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66 else:
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67 break
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68 stderr.close()
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69 #if rg aware, put files where they belong
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70 if options.new_files_path is not None:
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71 fastq_1_name = options.read_group_file_1
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72 fastq_2_name = options.read_group_file_2
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73 file_id_1 = options.file_id_1
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74 file_id_2 = options.file_id_2
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75 if file_id_2 is None:
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76 file_id_2 = file_id_1
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77 for filename in sorted( os.listdir( tmp_dir ) ):
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78 if filename.endswith( '_1.fastq' ):
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79 if fastq_1_name:
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80 shutil.move( os.path.join( tmp_dir, filename ), fastq_1_name )
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81 fastq_1_name = None
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82 else:
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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' )] ) ) )
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84 elif filename.endswith( '_2.fastq' ):
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85 if fastq_2_name:
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86 shutil.move( os.path.join( tmp_dir, filename ), fastq_2_name )
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87 fastq_2_name = None
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88 else:
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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' )] ) ) )
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90
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91 cleanup_before_exit( tmp_dir )
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92
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93 if __name__=="__main__": __main__()
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