Python PassingData.trioCallerReplicateConcordanceJob方法代码示例

本文整理汇总了Python中pymodule.PassingData.trioCallerReplicateConcordanceJob方法的典型用法代码示例。如果您正苦于以下问题：Python PassingData.trioCallerReplicateConcordanceJob方法的具体用法？Python PassingData.trioCallerReplicateConcordanceJob怎么用？Python PassingData.trioCallerReplicateConcordanceJob使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类pymodule.PassingData的用法示例。

在下文中一共展示了PassingData.trioCallerReplicateConcordanceJob方法的2个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。

示例1: mapEachInterval

# 需要导入模块: from pymodule import PassingData [as 别名]
# 或者: from pymodule.PassingData import trioCallerReplicateConcordanceJob [as 别名]

#.........这里部分代码省略.........
					extraDependentInputLs=None, \
					transferOutput=False, \
					extraArguments=None, \
					job_max_memory=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
							minJobPropertyValue=4000, maxJobPropertyValue=9000).value, \
					walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
							minJobPropertyValue=60, maxJobPropertyValue=1200).value,\
					)
		
		refineGenotypeOutputF = File(os.path.join(self.mapDirJob.folder, \
												'%s.trioCaller.vcf'%(intervalFileBasenamePrefix)))
		refineGenotypeJob = self.addTrioCallerJob(trioCallerWrapper=self.trioCallerWrapper, \
				trioCallerPath=self.trioCallerPath, \
				inputVCF=replicateVCFGenotypeColumnsJob.output,\
				pedFile=self.outputReplicatePedigreeJob.output, outputVCF=refineGenotypeOutputF, \
				inputPhased=True,\
				parentJobLs=[self.mapDirJob, replicateVCFGenotypeColumnsJob, self.outputReplicatePedigreeJob], \
				extraDependentInputLs=[], transferOutput=False, \
				extraArguments=None, \
				job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
							minJobPropertyValue=4000, maxJobPropertyValue=9000).value,\
				walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
							minJobPropertyValue=60, maxJobPropertyValue=1200).value)	#1.2G memory for 12K loci
		
		returnData.refineGenotypeJob = refineGenotypeJob
		
		"""
		2013.07.10 the TrioCaller VCF has some info tags that are not described in VCF header
		"""
		outputFile = File(os.path.join(self.mapDirJob.folder, \
												'%s.extraInfoDesc.vcf'%(intervalFileBasenamePrefix)))
		addInfoDescJob = self.addGenericJob(executable=self.AddMissingInfoDescriptionToVCFHeader, \
					inputFile=refineGenotypeJob.output, \
					inputArgumentOption="-i", \
					outputFile=outputFile, outputArgumentOption="-o", \
					parentJobLs=[self.mapDirJob, refineGenotypeJob], \
					extraDependentInputLs=None, extraOutputLs=None, \
					frontArgumentList=None, extraArguments=None, extraArgumentList=None, \
					transferOutput=False, sshDBTunnel=None, \
					key2ObjectForJob=None, objectWithDBArguments=None, \
					no_of_cpus=None, 
					job_max_memory=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=2000, \
							minJobPropertyValue=1000, maxJobPropertyValue=3000).value, \
					walltime=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
							minJobPropertyValue=60, maxJobPropertyValue=500).value,\
					max_walltime=None)
		
		# a CheckGenotypeConcordanceAmongReplicates.py job
		trioCallerReplicateConcordanceFile = File(os.path.join(self.statDirJob.folder, \
								'%s.trioCaller.concordance.tsv'%(intervalFileBasenamePrefix)))
		returnData.trioCallerReplicateConcordanceJob = self.addGATKJob(executable=self.CalculateConcordanceJava, \
					GenomeAnalysisTKJar=self.GenomeAnalysisTKJar, \
					GATKAnalysisType="CalculateConcordanceAmongReplicates",\
					inputFile=refineGenotypeJob.output, inputArgumentOption="--variant", \
					refFastaFList=self.registerReferenceData.refFastaFList, \
					interval=None, \
					outputFile=trioCallerReplicateConcordanceFile, outputArgumentOption="--concordanceStatFname",\
					frontArgumentList=None, extraArguments="--replicateIndividualTag %s"%(self.replicateIndividualTag), \
					extraArgumentList=None, extraOutputLs=None, \
					parentJobLs=[self.statDirJob, refineGenotypeJob], \
					transferOutput=False, \
					no_of_cpus=None, \
					job_max_memory=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=6000, \
							minJobPropertyValue=9000, maxJobPropertyValue=16000).value, \
					walltime=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
							minJobPropertyValue=60, maxJobPropertyValue=1200).value)
		
		
		#2013.06.14
		#merge replicates to generate consensus call
		# (not haplotype-based, as different recombination points across replicate haplotypes make it non-trivial )
		mergeReplicateOutputF = File(os.path.join(self.mapDirJob.folder, \
									'%s.replicatesMerged.vcf'%(intervalFileBasenamePrefix)))
		returnData.mergeVCFReplicateColumnsJob = self.addMergeVCFReplicateGenotypeColumnsJob(\
							executable=self.MergeVCFReplicateHaplotypesJava,\
							GenomeAnalysisTKJar=self.GenomeAnalysisTKJar, \
							inputF=addInfoDescJob.output, outputF=mergeReplicateOutputF, \
							replicateIndividualTag=self.replicateIndividualTag, \
							refFastaFList=self.registerReferenceData.refFastaFList, \
							parentJobLs=[self.mapDirJob, addInfoDescJob], \
							extraDependentInputLs=[], transferOutput=False, \
							extraArguments=None, \
							analysis_type='MergeVCFReplicateGenotypeColumns',\
					job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
							minJobPropertyValue=5000, maxJobPropertyValue=9000).value,\
					walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
							minJobPropertyValue=60, maxJobPropertyValue=1200).value)
		
		
		return returnData

开发者ID:mjmontague，项目名称:vervet-web，代码行数:104，代码来源:BeagleAndTrioCallerOnVCFWorkflow.py

示例2: addRefineGenotypeJobsViaTrioCaller

# 需要导入模块: from pymodule import PassingData [as 别名]
# 或者: from pymodule.PassingData import trioCallerReplicateConcordanceJob [as 别名]

#.........这里部分代码省略.........
					transferOutput=False, \
					extraArguments=None, \
					job_max_memory=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
							minJobPropertyValue=4000, maxJobPropertyValue=9000).value, \
					walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
							minJobPropertyValue=60, maxJobPropertyValue=1200).value,\
					)
		
		trioCallerOutputFile = File(os.path.join(outputDirJob.folder, \
												'%s.trioCaller.vcf'%(vcfBaseFname)))
		trioCallerJob = self.addTrioCallerJob(trioCallerWrapper=self.trioCallerWrapper, \
				trioCallerPath=self.trioCallerPath, \
				inputVCF=replicateVCFGenotypeColumnsJob.output,\
				pedFile=self.outputPedigreeJob.output, outputVCF=trioCallerOutputFile, \
				inputPhased=False,\
				parentJobLs=[outputDirJob, replicateVCFGenotypeColumnsJob, self.outputPedigreeJob], \
				extraDependentInputLs=[], transferOutput=False, \
				extraArguments=None, \
				job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
							minJobPropertyValue=4000, maxJobPropertyValue=9000).value,\
				walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
							minJobPropertyValue=60, maxJobPropertyValue=1200).value)	#1.2G memory for 12K loci
		
		returnData.trioCallerJob = trioCallerJob
		
		"""
		2013.07.10 the TrioCaller VCF has some info tags that are not described in VCF header
		"""
		outputFile = File(os.path.join(outputDirJob.folder, \
												'%s.extraInfoDesc.vcf'%(vcfBaseFname)))
		addInfoDescJob = self.addGenericJob(executable=self.AddMissingInfoDescriptionToVCFHeader, \
					inputFile=trioCallerJob.output, \
					inputArgumentOption="-i", \
					outputFile=outputFile, outputArgumentOption="-o", \
					parentJobLs=[outputDirJob, trioCallerJob], \
					extraDependentInputLs=None, extraOutputLs=None, \
					frontArgumentList=None, extraArguments=None, extraArgumentList=None, \
					transferOutput=False, sshDBTunnel=None, \
					key2ObjectForJob=None, objectWithDBArguments=None, \
					no_of_cpus=None, 
					job_max_memory=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=2000, \
							minJobPropertyValue=1000, maxJobPropertyValue=3000).value, \
					walltime=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
							minJobPropertyValue=60, maxJobPropertyValue=500).value,\
					max_walltime=None)
		
		if statDirJob:
			# a CheckGenotypeConcordanceAmongReplicates.py job
			trioCallerReplicateConcordanceFile = File(os.path.join(self.statDirJob.folder, \
									'%s.trioCaller.concordance.tsv'%(vcfBaseFname)))
			returnData.trioCallerReplicateConcordanceJob = self.addGATKJob(executable=self.CalculateConcordanceJava, \
						GenomeAnalysisTKJar=self.GenomeAnalysisTKJar, \
						GATKAnalysisType="CalculateConcordanceAmongReplicates",\
						inputFile=trioCallerJob.output, inputArgumentOption="--variant", \
						refFastaFList=self.registerReferenceData.refFastaFList, \
						interval=None, \
						outputFile=trioCallerReplicateConcordanceFile, outputArgumentOption="--concordanceStatFname",\
						frontArgumentList=None, extraArguments="--replicateIndividualTag %s"%(self.replicateIndividualTag), \
						extraArgumentList=None, extraOutputLs=None, \
						parentJobLs=[self.statDirJob, trioCallerJob], \
						transferOutput=False, \
						no_of_cpus=None, \
						job_max_memory=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
								baseInputVolume=baseInputVolume, baseJobPropertyValue=6000, \
								minJobPropertyValue=9000, maxJobPropertyValue=16000).value, \
						walltime=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
								baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
								minJobPropertyValue=60, maxJobPropertyValue=1200).value)
			
		
		#2013.06.14
		#merge replicates to generate consensus call
		# (not haplotype-based, as different recombination points across replicate haplotypes make it non-trivial )
		mergeReplicateOutputF = File(os.path.join(outputDirJob.folder, \
									'%s.replicatesMerged.vcf'%(vcfBaseFname)))
		mergeVCFReplicateColumnsJob = self.addMergeVCFReplicateGenotypeColumnsJob(\
							executable=self.MergeVCFReplicateHaplotypesJava,\
							GenomeAnalysisTKJar=self.GenomeAnalysisTKJar, \
							inputF=addInfoDescJob.output, outputF=mergeReplicateOutputF, \
							replicateIndividualTag=self.replicateIndividualTag, \
							refFastaFList=self.registerReferenceData.refFastaFList, \
							parentJobLs=[outputDirJob, addInfoDescJob], \
							extraDependentInputLs=[], transferOutput=False, \
							extraArguments=None, \
							analysis_type='MergeVCFReplicateGenotypeColumns',\
					job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
							minJobPropertyValue=5000, maxJobPropertyValue=9000).value,\
					walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
							baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
							minJobPropertyValue=60, maxJobPropertyValue=1200).value)
		returnData.refineGenotypeJob = mergeVCFReplicateColumnsJob	#the final gentoype job
		returnData.refineGenotypeJob.intervalData = intervalData	#attached so that it could be used by downstream jobs
		return returnData

开发者ID:mjmontague，项目名称:vervet-web，代码行数:104，代码来源:AlignmentToTrioCallPipeline.py

注：本文中的pymodule.PassingData.trioCallerReplicateConcordanceJob方法示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。