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1 #!/usr/bin/env python
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2 # David Hoover, based on gatk by Dan Blankenberg
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3 """
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4 A wrapper script for running the GenomeAnalysisTK.jar commands.
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5 """
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6
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7 import optparse
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8 import os
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9 import shutil
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10 import subprocess
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11 import sys
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12 import tempfile
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13 from binascii import unhexlify
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14
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15 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
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16 GALAXY_EXT_TO_GATK_FILE_TYPE = GALAXY_EXT_TO_GATK_EXT # for now, these are the same, but could be different if needed
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17 DEFAULT_GATK_PREFIX = "gatk_file"
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18 CHUNK_SIZE = 2**20 # 1mb
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19
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20
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21 def cleanup_before_exit( tmp_dir ):
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22 if tmp_dir and os.path.exists( tmp_dir ):
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23 shutil.rmtree( tmp_dir )
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24
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25
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26 def gatk_filename_from_galaxy( galaxy_filename, galaxy_ext, target_dir=None, prefix=None ):
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27 suffix = GALAXY_EXT_TO_GATK_EXT.get( galaxy_ext, galaxy_ext )
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28 if prefix is None:
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29 prefix = DEFAULT_GATK_PREFIX
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30 if target_dir is None:
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31 target_dir = os.getcwd()
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32 gatk_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) )
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33 os.symlink( galaxy_filename, gatk_filename )
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34 return gatk_filename
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35
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36
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37 def gatk_filetype_argument_substitution( argument, galaxy_ext ):
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38 return argument % dict( file_type=GALAXY_EXT_TO_GATK_FILE_TYPE.get( galaxy_ext, galaxy_ext ) )
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39
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40
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41 def open_file_from_option( filename, mode='rb' ):
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42 if filename:
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43 return open( filename, mode=mode )
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44 return None
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45
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46
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47 def html_report_from_directory( html_out, dir ):
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48 html_out.write( '<html>\n<head>\n<title>Galaxy - GATK Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' )
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49 for fname in sorted( os.listdir( dir ) ):
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50 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) )
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51 html_out.write( '</ul>\n</body>\n</html>\n' )
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52
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53
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54 def index_bam_files( bam_filenames ):
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55 for bam_filename in bam_filenames:
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56 bam_index_filename = "%s.bai" % bam_filename
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57 if not os.path.exists( bam_index_filename ):
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58 # need to index this bam file
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59 stderr_name = tempfile.NamedTemporaryFile( prefix="bam_index_stderr" ).name
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60 command = 'samtools index %s %s' % ( bam_filename, bam_index_filename )
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61 try:
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62 subprocess.check_call( args=command, shell=True, stderr=open( stderr_name, 'wb' ) )
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63 except:
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64 for line in open( stderr_name ):
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65 print >> sys.stderr, line
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66 raise Exception( "Error indexing BAM file" )
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67 finally:
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68 os.unlink( stderr_name )
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69
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70
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71 def __main__():
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72 # Parse Command Line
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73 parser = optparse.OptionParser()
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74 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.' )
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75 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.' )
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76 parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' )
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77 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.' )
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78 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.' )
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79 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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80 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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81 parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"')
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82 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)' )
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83 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)' )
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84 (options, args) = parser.parse_args()
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85
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86 if options.pass_through_options:
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87 cmd = ' '.join( options.pass_through_options )
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88 else:
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89 cmd = ''
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90 if options.pass_through_options_encoded:
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91 cmd = '%s %s' % ( cmd, ' '.join( map( unhexlify, options.pass_through_options_encoded ) ) )
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92 if options.max_jvm_heap is not None:
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93 cmd = cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 )
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94 elif options.max_jvm_heap_fraction is not None:
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95 cmd = cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 )
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96 bam_filenames = []
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97 tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' )
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98 try:
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99 if options.datasets:
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100 for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets:
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101 gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir=tmp_dir, prefix=prefix )
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102 if dataset_arg:
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103 cmd = '%s %s "%s"' % ( cmd, gatk_filetype_argument_substitution( dataset_arg, galaxy_ext ), gatk_filename )
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104 if galaxy_ext == "bam":
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105 bam_filenames.append( gatk_filename )
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106 if galaxy_ext == 'fasta':
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107 subprocess.check_call( 'samtools faidx "%s"' % gatk_filename, shell=True )
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108 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 )
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109 index_bam_files( bam_filenames )
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110 # set up stdout and stderr output options
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111 stdout = open_file_from_option( options.stdout, mode='wb' )
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112 stderr = open_file_from_option( options.stderr, mode='wb' )
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113 # if no stderr file is specified, we'll use our own
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114 if stderr is None:
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115 stderr = tempfile.NamedTemporaryFile( prefix="gatk-stderr-", dir=tmp_dir )
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116
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117 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir )
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118 return_code = proc.wait()
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119
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120 if return_code:
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121 stderr_target = sys.stderr
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122 else:
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123 stderr_target = sys.stdout
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124 stderr.flush()
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125 stderr.seek(0)
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126 while True:
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127 chunk = stderr.read( CHUNK_SIZE )
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128 if chunk:
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129 stderr_target.write( chunk )
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130 else:
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131 break
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132 stderr.close()
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133 finally:
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134 cleanup_before_exit( tmp_dir )
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135
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136 # generate html reports
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137 if options.html_report_from_directory:
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138 for ( html_filename, html_dir ) in options.html_report_from_directory:
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139 html_report_from_directory( open( html_filename, 'wb' ), html_dir )
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140
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141
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142 if __name__ == "__main__":
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143 __main__()
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