Mercurial > repos > iuc > gatk2
annotate gatk2_wrapper.py @ 6:35c00763cb5c draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
| author | iuc |
|---|---|
| date | Mon, 04 Jun 2018 05:38:15 -0400 |
| parents | f244b8209eb8 |
| children |
| rev | line source |
|---|---|
| 0 | 1 #!/usr/bin/env python |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
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changeset
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2 # David Hoover, based on gatk by Dan Blankenberg |
| 0 | 3 """ |
| 4 A wrapper script for running the GenomeAnalysisTK.jar commands. | |
| 5 """ | |
| 6 | |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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7 import optparse |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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8 import os |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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9 import shutil |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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10 import subprocess |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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11 import sys |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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12 import tempfile |
| 0 | 13 from binascii import unhexlify |
| 14 | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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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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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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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 |
| 0 | 17 DEFAULT_GATK_PREFIX = "gatk_file" |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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18 CHUNK_SIZE = 2**20 # 1mb |
| 0 | 19 |
| 20 | |
| 21 def cleanup_before_exit( tmp_dir ): | |
| 22 if tmp_dir and os.path.exists( tmp_dir ): | |
| 23 shutil.rmtree( tmp_dir ) | |
| 24 | |
| 4 | 25 |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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26 def gatk_filename_from_galaxy( galaxy_filename, galaxy_ext, target_dir=None, prefix=None ): |
| 0 | 27 suffix = GALAXY_EXT_TO_GATK_EXT.get( galaxy_ext, galaxy_ext ) |
| 28 if prefix is None: | |
| 29 prefix = DEFAULT_GATK_PREFIX | |
| 30 if target_dir is None: | |
| 31 target_dir = os.getcwd() | |
| 32 gatk_filename = os.path.join( target_dir, "%s.%s" % ( prefix, suffix ) ) | |
| 33 os.symlink( galaxy_filename, gatk_filename ) | |
| 34 return gatk_filename | |
| 35 | |
| 4 | 36 |
| 0 | 37 def gatk_filetype_argument_substitution( argument, galaxy_ext ): |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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38 return argument % dict( file_type=GALAXY_EXT_TO_GATK_FILE_TYPE.get( galaxy_ext, galaxy_ext ) ) |
| 0 | 39 |
| 4 | 40 |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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41 def open_file_from_option( filename, mode='rb' ): |
| 0 | 42 if filename: |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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43 return open( filename, mode=mode ) |
| 0 | 44 return None |
| 45 | |
| 4 | 46 |
| 0 | 47 def html_report_from_directory( html_out, dir ): |
| 48 html_out.write( '<html>\n<head>\n<title>Galaxy - GATK Output</title>\n</head>\n<body>\n<p/>\n<ul>\n' ) | |
| 49 for fname in sorted( os.listdir( dir ) ): | |
| 50 html_out.write( '<li><a href="%s">%s</a></li>\n' % ( fname, fname ) ) | |
| 51 html_out.write( '</ul>\n</body>\n</html>\n' ) | |
| 52 | |
| 4 | 53 |
| 54 def index_bam_files( bam_filenames ): | |
| 0 | 55 for bam_filename in bam_filenames: |
| 56 bam_index_filename = "%s.bai" % bam_filename | |
| 57 if not os.path.exists( bam_index_filename ): | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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58 # need to index this bam file |
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35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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59 stderr_name = tempfile.NamedTemporaryFile( prefix="bam_index_stderr" ).name |
| 0 | 60 command = 'samtools index %s %s' % ( bam_filename, bam_index_filename ) |
| 4 | 61 try: |
| 62 subprocess.check_call( args=command, shell=True, stderr=open( stderr_name, 'wb' ) ) | |
| 63 except: | |
| 0 | 64 for line in open( stderr_name ): |
| 65 print >> sys.stderr, line | |
| 66 raise Exception( "Error indexing BAM file" ) | |
| 4 | 67 finally: |
| 68 os.unlink( stderr_name ) | |
| 0 | 69 |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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70 |
| 0 | 71 def __main__(): |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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72 # Parse Command Line |
| 0 | 73 parser = optparse.OptionParser() |
| 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.' ) | |
| 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.' ) | |
| 76 parser.add_option( '-d', '--dataset', dest='datasets', action='append', type="string", nargs=4, help='"-argument" "original_filename" "galaxy_filetype" "name_prefix"' ) | |
| 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.' ) | |
| 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.' ) | |
| 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.' ) | |
| 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.' ) | |
| 81 parser.add_option( '', '--html_report_from_directory', dest='html_report_from_directory', action='append', type="string", nargs=2, help='"Target HTML File" "Directory"') | |
| 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)' ) | |
| 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)' ) | |
| 84 (options, args) = parser.parse_args() | |
| 4 | 85 |
| 0 | 86 if options.pass_through_options: |
| 87 cmd = ' '.join( options.pass_through_options ) | |
| 88 else: | |
| 89 cmd = '' | |
| 90 if options.pass_through_options_encoded: | |
| 91 cmd = '%s %s' % ( cmd, ' '.join( map( unhexlify, options.pass_through_options_encoded ) ) ) | |
| 92 if options.max_jvm_heap is not None: | |
| 93 cmd = cmd.replace( 'java ', 'java -Xmx%s ' % ( options.max_jvm_heap ), 1 ) | |
| 94 elif options.max_jvm_heap_fraction is not None: | |
| 95 cmd = cmd.replace( 'java ', 'java -XX:DefaultMaxRAMFraction=%s -XX:+UseParallelGC ' % ( options.max_jvm_heap_fraction ), 1 ) | |
| 96 bam_filenames = [] | |
| 4 | 97 tmp_dir = tempfile.mkdtemp( prefix='tmp-gatk-' ) |
| 98 try: | |
| 99 if options.datasets: | |
| 100 for ( dataset_arg, filename, galaxy_ext, prefix ) in options.datasets: | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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101 gatk_filename = gatk_filename_from_galaxy( filename, galaxy_ext, target_dir=tmp_dir, prefix=prefix ) |
| 4 | 102 if dataset_arg: |
| 103 cmd = '%s %s "%s"' % ( cmd, gatk_filetype_argument_substitution( dataset_arg, galaxy_ext ), gatk_filename ) | |
| 104 if galaxy_ext == "bam": | |
| 105 bam_filenames.append( gatk_filename ) | |
| 106 if galaxy_ext == 'fasta': | |
| 107 subprocess.check_call( 'samtools faidx "%s"' % gatk_filename, shell=True ) | |
| 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 ) | |
| 109 index_bam_files( bam_filenames ) | |
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6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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110 # set up stdout and stderr output options |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
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111 stdout = open_file_from_option( options.stdout, mode='wb' ) |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
112 stderr = open_file_from_option( options.stderr, mode='wb' ) |
|
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
113 # if no stderr file is specified, we'll use our own |
| 4 | 114 if stderr is None: |
| 115 stderr = tempfile.NamedTemporaryFile( prefix="gatk-stderr-", dir=tmp_dir ) | |
| 116 | |
| 117 proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) | |
| 118 return_code = proc.wait() | |
| 119 | |
| 120 if return_code: | |
| 121 stderr_target = sys.stderr | |
| 0 | 122 else: |
| 4 | 123 stderr_target = sys.stdout |
| 124 stderr.flush() | |
| 125 stderr.seek(0) | |
| 126 while True: | |
| 127 chunk = stderr.read( CHUNK_SIZE ) | |
| 128 if chunk: | |
| 129 stderr_target.write( chunk ) | |
| 130 else: | |
| 131 break | |
| 132 stderr.close() | |
| 133 finally: | |
| 134 cleanup_before_exit( tmp_dir ) | |
| 135 | |
|
6
35c00763cb5c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gatk2 commit cf399638ebca4250bcc15f468238a9964de97b33
iuc
parents:
4
diff
changeset
|
136 # generate html reports |
| 0 | 137 if options.html_report_from_directory: |
| 138 for ( html_filename, html_dir ) in options.html_report_from_directory: | |
| 139 html_report_from_directory( open( html_filename, 'wb' ), html_dir ) | |
| 4 | 140 |
| 0 | 141 |
| 4 | 142 if __name__ == "__main__": |
| 143 __main__() |