Mercurial > repos > mini > strelka
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author | mini |
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date | Mon, 01 Dec 2014 12:22:18 +0100 |
parents | 1c8dcda28be7 |
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#!/usr/bin/env python #Gregoire Seguin-Henry (Engineer IT) #Amine Sbitti (Data Scientist) #Ludovic Marie-Sainte (Project Manager) #For Geviteam 2014 """ A wrapper script for running the GenomeAnalysisTK.jar commands. """ from __future__ import print_function import sys, argparse, os, tempfile, subprocess, shutil from binascii import unhexlify from string import Template from galaxy import eggs def cleanup_before_exit( tmp_dir ): if tmp_dir and os.path.exists( tmp_dir ): shutil.rmtree( tmp_dir ) def _create_config(args, config_path): conf_file = open(config_path, "w") conf_file.write("[user]\n") args2 = vars(args) for option in args2: if not option in ["tumorBam", "normalBam", "refFile", "configFile", "scriptPath", "a", "b", "c", "d", "e", "extraStrelkaArguments"] and args2[option]!=None: conf_file.write("%s=%s\n" % (option, args2[option])) if args.extraStrelkaArguments == "yes": conf_file.write("extraStrelkaArguments=") if args.a: conf_file.write("--ignore-conflicting-read-names ") if args.b != None: conf_file.write("-used-allele-count-min-qscore %s " % (args.b)) if args.c != None: conf_file.write("--candidate-indel-input-vcf %s " % (args.c)) if args.d != None: conf_file.write("--force-output-vcf %s " % (args.d)) if args.e != None: conf_file.write("-min-small-candidate-indel-read-frac %s " % (args.e)) conf_file.write("\n") conf_file.close() def my_Popen(cmd, prefix_for_stderr_name, tmp_dir, msg_error): stderr_name = tempfile.NamedTemporaryFile( prefix = prefix_for_stderr_name ).name proc = subprocess.Popen( args=cmd, shell=True, stderr=open( stderr_name, 'wb' ) ) return_code = proc.wait() if return_code: for line in open( stderr_name ): print(line, file=sys.stderr) os.unlink( stderr_name ) #clean up cleanup_before_exit( tmp_dir ) raise Exception( msg_error ) else: os.unlink( stderr_name ) def index_bam_files( bam_filenames, tmp_dir ): for bam_filename in bam_filenames: bam_index_filename = "%s.bai" % bam_filename print("bam_filename is: " + bam_filename + " bam_index_filename is: " + bam_index_filename + " test is: %s" % os.path.exists(bam_index_filename)) if not os.path.exists( bam_index_filename ): #need to index this bam file command = 'samtools index %s %s' % ( bam_filename, bam_index_filename ) my_Popen( command, "bam_index_stderr", tmp_dir, "Error during indexation of fasta file :" + bam_filename) def index_fasta_files( fasta_filenames, tmp_dir ): for fasta_filename in fasta_filenames: fasta_index_filename = "%s.fai" % fasta_filename print("fasta_filename is: " + fasta_filename + " fasta_index_filename is: " + fasta_index_filename + " test is: %s" % os.path.exists(fasta_index_filename)) if not os.path.exists( fasta_index_filename ): #need to index this bam file command = 'samtools faidx %s %s' % ( fasta_filename, fasta_index_filename ) my_Popen( command, "fasta_index_stderr", tmp_dir, "Error during indexation of fasta file :" + fasta_filename) def __main__(): #Manage options print(os.environ['PATH']) parser = argparse.ArgumentParser() parser.add_argument( '--tumorBam', help='path to tumor bam file', required = False ) parser.add_argument( '--normalBam', help='', required = False ) parser.add_argument( '--refFile', help='', required = False ) parser.add_argument( '--configFile', help='', required = False ) parser.add_argument( '--depthFilterMultiple', help='', required = False ) parser.add_argument( '--snvMaxFilteredBasecallFrac', help='', required = False ) parser.add_argument( '--snvMaxSpanningDeletionFrac', help='', required = False ) parser.add_argument( '--indelMaxRefRepeat', help='', required = False ) parser.add_argument( '--indelMaxWindowFilteredBasecallFrac', help='', required = False ) parser.add_argument( '--indelMaxIntHpolLength', help='', required = False ) parser.add_argument( '--ssnvPrior', help='', required = False ) parser.add_argument( '--sindelPrior', help='', required = False ) parser.add_argument( '--ssnvNoise', help='', required = False ) parser.add_argument( '--sindelNoise', help='', required = False ) parser.add_argument( '--ssnvNoiseStrandBiasFrac', help='', required = False ) parser.add_argument( '--minTier1Mapq', help='', required = False ) parser.add_argument( '--minTier2Mapq', help='', required = False ) parser.add_argument( '--ssnvQuality_LowerBound', help='', required = False ) parser.add_argument( '--sindelQuality_LowerBound', help='', required = False ) parser.add_argument( '--isWriteRealignedBam', help='', required = False ) parser.add_argument( '--binSize', help='path to tumor bam file', required = False ) parser.add_argument( '--extraStrelkaArguments', help='', required = False ) parser.add_argument( '--isSkipDepthFilters', help='', required = False ) parser.add_argument( '--maxInputDepth', help='', required = False ) parser.add_argument( '--scriptPath', help='', required = False ) parser.add_argument( '-a', action="store_true", help='', required = False ) parser.add_argument( '-b', help='', required = False ) parser.add_argument( '-c', help='', required = False ) parser.add_argument( '-d', help='', required = False ) parser.add_argument( '-e', help='', required = False ) args = parser.parse_args() root_dir= args.scriptPath expected_dir="for_tests" job_dir=os.getcwd() analysis_dir=job_dir + "/StrelkaAnalysis" config_script=root_dir + "/configureStrelkaWorkflow.pl" tmp_dir = tempfile.mkdtemp( prefix='tmp-strelkaAnalysis-' ) config_ini = "%s/config.ini" % (tmp_dir) print("root_dir: " + root_dir + "\njob_dir :" + job_dir + "\nanalysis_dir :" + analysis_dir + "\nconfig_script :" + config_script + "\ntmp_dir :" + tmp_dir + "\nconfig_ini :" + config_ini) #verifying eveything's ok if not os.path.isfile(config_script): sys.exit("ERROR: The strelka workflow must be built prior to running. See installation instructions in '$root_dir/README'") print("configuring...", file=sys.stdout) if os.path.exists(analysis_dir): sys.exit("'" + analysis_dir + "' already exist, if you are executing this tool from galaxy it should not happen") # creating index if needed bam_filenames = [ args.tumorBam, args.normalBam ] index_bam_files( bam_filenames, tmp_dir ) fasta_files = [ args.refFile ] index_fasta_files( fasta_files, tmp_dir ) #creating config file if needed if args.configFile == "Custom": _create_config(args, config_ini) elif args.configFile in ["strelka_config_bwa_default.ini", "strelka_config_isaac_default.ini", "strelka_config_eland_default.ini"]: cmdbash="cp %s %s" % (root_dir + "/lib/" + args.configFile, config_ini) my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of default config file, maybe it was removed") else: if not os.path.exists(args.configFile): print( "The path to your configuration File seems to be wrong, use another one or custom option", file=sys.stderr) cmdbash="cp %s %s" % (args.configFile, config_ini) my_Popen(cmdbash, "copy_default_file_err", tmp_dir, "Error during the copy of the selected config file") #configuration of workflow cmd="%s --tumor=%s --normal=%s --ref=%s --config=%s --output-dir=%s" % (config_script, args.tumorBam, args.normalBam, args.refFile, config_ini, analysis_dir) print( "**** Starting configuration.") print( "**** Configuration cmd: '" + cmd + "'") my_Popen( cmd, "cinfugation_stderr", tmp_dir, "Error during configuration !") print("completed configuration") #run the workflow ! cmd="make -C " + analysis_dir print("**** starting workflow.") print("**** workflow cmd: '" + cmd + "'") my_Popen( cmd, "workflow_stderr", tmp_dir, "Error during workflow execution !") print("**** completed workflow execution") cmdbash="cp %s %s" % (config_ini, analysis_dir + "/config.ini") my_Popen(cmdbash, "copy_final_conf_file_err", tmp_dir, "Error during the copy of conf file after job is done, quite strange...") if __name__=='__main__': __main__()