Mercurial > repos > mini > strelka
comparison strelka_wrapper.py @ 22:1c8dcda28be7
version 27/11/2014, corrected extra arguments bug
| author | mini |
|---|---|
| date | Thu, 27 Nov 2014 10:31:58 +0100 |
| parents | 3c10d88b55ad |
| children |
comparison
equal
deleted
inserted
replaced
| 21:f785839fb395 | 22:1c8dcda28be7 |
|---|---|
| 18 shutil.rmtree( tmp_dir ) | 18 shutil.rmtree( tmp_dir ) |
| 19 | 19 |
| 20 def _create_config(args, config_path): | 20 def _create_config(args, config_path): |
| 21 conf_file = open(config_path, "w") | 21 conf_file = open(config_path, "w") |
| 22 conf_file.write("[user]\n") | 22 conf_file.write("[user]\n") |
| 23 for option in args: | 23 args2 = vars(args) |
| 24 if not option in ["tumorBam", "normalBam", "refFile", "configFile", "scriptPath"] and args[option]!=None: | 24 for option in args2: |
| 25 conf_file.write("%s=%s\n" % (option, args[option])) | 25 if not option in ["tumorBam", "normalBam", "refFile", "configFile", "scriptPath", "a", "b", "c", "d", "e", "extraStrelkaArguments"] and args2[option]!=None: |
| 26 conf_file.write("%s=%s\n" % (option, args2[option])) | |
| 27 if args.extraStrelkaArguments == "yes": | |
| 28 conf_file.write("extraStrelkaArguments=") | |
| 29 if args.a: | |
| 30 conf_file.write("--ignore-conflicting-read-names ") | |
| 31 if args.b != None: | |
| 32 conf_file.write("-used-allele-count-min-qscore %s " % (args.b)) | |
| 33 if args.c != None: | |
| 34 conf_file.write("--candidate-indel-input-vcf %s " % (args.c)) | |
| 35 if args.d != None: | |
| 36 conf_file.write("--force-output-vcf %s " % (args.d)) | |
| 37 if args.e != None: | |
| 38 conf_file.write("-min-small-candidate-indel-read-frac %s " % (args.e)) | |
| 39 conf_file.write("\n") | |
| 26 conf_file.close() | 40 conf_file.close() |
| 27 | 41 |
| 28 def my_Popen(cmd, prefix_for_stderr_name, tmp_dir, msg_error): | 42 def my_Popen(cmd, prefix_for_stderr_name, tmp_dir, msg_error): |
| 29 stderr_name = tempfile.NamedTemporaryFile( prefix = prefix_for_stderr_name ).name | 43 stderr_name = tempfile.NamedTemporaryFile( prefix = prefix_for_stderr_name ).name |
| 30 proc = subprocess.Popen( args=cmd, shell=True, stderr=open( stderr_name, 'wb' ) ) | 44 proc = subprocess.Popen( args=cmd, shell=True, stderr=open( stderr_name, 'wb' ) ) |
| 58 | 72 |
| 59 def __main__(): | 73 def __main__(): |
| 60 #Manage options | 74 #Manage options |
| 61 print(os.environ['PATH']) | 75 print(os.environ['PATH']) |
| 62 parser = argparse.ArgumentParser() | 76 parser = argparse.ArgumentParser() |
| 63 parser.add_argument( '-t', '--tumorBam', help='path to tumor bam file', required = False ) | 77 parser.add_argument( '--tumorBam', help='path to tumor bam file', required = False ) |
| 64 parser.add_argument( '-n', '--normalBam', help='', required = False ) | 78 parser.add_argument( '--normalBam', help='', required = False ) |
| 65 parser.add_argument( '-r', '--refFile', help='', required = False ) | 79 parser.add_argument( '--refFile', help='', required = False ) |
| 66 parser.add_argument( '-c', '--configFile', help='', required = False ) | 80 parser.add_argument( '--configFile', help='', required = False ) |
| 67 parser.add_argument( '--depthFilterMultiple', help='', required = False ) | 81 parser.add_argument( '--depthFilterMultiple', help='', required = False ) |
| 68 parser.add_argument( '--snvMaxFilteredBasecallFrac', help='', required = False ) | 82 parser.add_argument( '--snvMaxFilteredBasecallFrac', help='', required = False ) |
| 69 parser.add_argument( '--snvMaxSpanningDeletionFrac', help='', required = False ) | 83 parser.add_argument( '--snvMaxSpanningDeletionFrac', help='', required = False ) |
| 70 parser.add_argument( '--indelMaxRefRepeat', help='', required = False ) | 84 parser.add_argument( '--indelMaxRefRepeat', help='', required = False ) |
| 71 parser.add_argument( '--indelMaxWindowFilteredBasecallFrac', help='', required = False ) | 85 parser.add_argument( '--indelMaxWindowFilteredBasecallFrac', help='', required = False ) |
| 83 parser.add_argument( '--binSize', help='path to tumor bam file', required = False ) | 97 parser.add_argument( '--binSize', help='path to tumor bam file', required = False ) |
| 84 parser.add_argument( '--extraStrelkaArguments', help='', required = False ) | 98 parser.add_argument( '--extraStrelkaArguments', help='', required = False ) |
| 85 parser.add_argument( '--isSkipDepthFilters', help='', required = False ) | 99 parser.add_argument( '--isSkipDepthFilters', help='', required = False ) |
| 86 parser.add_argument( '--maxInputDepth', help='', required = False ) | 100 parser.add_argument( '--maxInputDepth', help='', required = False ) |
| 87 parser.add_argument( '--scriptPath', help='', required = False ) | 101 parser.add_argument( '--scriptPath', help='', required = False ) |
| 102 parser.add_argument( '-a', action="store_true", help='', required = False ) | |
| 103 parser.add_argument( '-b', help='', required = False ) | |
| 104 parser.add_argument( '-c', help='', required = False ) | |
| 105 parser.add_argument( '-d', help='', required = False ) | |
| 106 parser.add_argument( '-e', help='', required = False ) | |
| 88 args = parser.parse_args() | 107 args = parser.parse_args() |
| 89 | 108 |
| 90 root_dir= args.scriptPath | 109 root_dir= args.scriptPath |
| 91 expected_dir="for_tests" | 110 expected_dir="for_tests" |
| 92 job_dir=os.getcwd() | 111 job_dir=os.getcwd() |
| 112 fasta_files = [ args.refFile ] | 131 fasta_files = [ args.refFile ] |
| 113 index_fasta_files( fasta_files, tmp_dir ) | 132 index_fasta_files( fasta_files, tmp_dir ) |
| 114 | 133 |
| 115 #creating config file if needed | 134 #creating config file if needed |
| 116 if args.configFile == "Custom": | 135 if args.configFile == "Custom": |
| 117 _create_config(vars(args), config_ini) | 136 _create_config(args, config_ini) |
| 118 elif args.configFile in ["strelka_config_bwa_default.ini", "strelka_config_isaac_default.ini", "strelka_config_eland_default.ini"]: | 137 elif args.configFile in ["strelka_config_bwa_default.ini", "strelka_config_isaac_default.ini", "strelka_config_eland_default.ini"]: |
| 119 cmdbash="cp %s %s" % (root_dir + "/lib/" + args.configFile, config_ini) | 138 cmdbash="cp %s %s" % (root_dir + "/lib/" + args.configFile, config_ini) |
| 120 my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed") | 139 my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed") |
| 121 else: | 140 else: |
| 122 if not os.path.exists(args.configFile): | 141 if not os.path.exists(args.configFile): |