def __init__(self, **keywords):
"""
2011-7-11
"""
#if self.option_default_dict.get('ligateVcfPerlPath'):
# self.pathToInsertHomePathList.append('ligateVcfPerlPath')
AbstractVervetWorkflow.__init__(self, **keywords)
def registerCustomExecutables(self, workflow=None): """ 2011-11-28 """ if workflow==None: workflow=self AbstractVervetWorkflow.registerCustomExecutables(self, workflow) namespace = workflow.namespace version = workflow.version operatingSystem = workflow.operatingSystem architecture = workflow.architecture clusters_size = workflow.clusters_size site_handler = workflow.site_handler vervetSrcPath = self.vervetSrcPath executableClusterSizeMultiplierList = [] #2012.8.7 each cell is a tuple of (executable, clusterSizeMultipler (0 if u do not need clustering) #mergeSameHeaderTablesIntoOne is used here on per chromosome basis, so allow clustering executableClusterSizeMultiplierList.append((workflow.mergeSameHeaderTablesIntoOne, 1)) self.addExecutableAndAssignProperClusterSize(executableClusterSizeMultiplierList, defaultClustersSize=self.clusters_size) if self.plinkIBDCheckOutputFname: self.plinkIBDCheckOutputFile = self.registerOneInputFile(workflow=workflow, inputFname=self.plinkIBDCheckOutputFname, input_site_handler=None, \ folderName=self.pegasusFolderName) else: self.plinkIBDCheckOutputFile = None
def __init__(self, **keywords): """ 2011-7-11 """ AbstractVervetWorkflow.__init__(self, **keywords) """
def preReduce(self, workflow=None, outputDirPrefix="", passingData=None, transferOutput=True, **keywords): """ 2012.9.17 """ returnData = AbstractVervetWorkflow.preReduce(self, workflow=workflow, outputDirPrefix=outputDirPrefix,\ passingData=passingData, transferOutput=transferOutput, **keywords) frequencyDirJob = self.addMkDirJob(outputDir="%sFrequency"%(outputDirPrefix)) passingData.frequencyDirJob = frequencyDirJob #ExtractSamplesFromVCF for the 1st population extractPop1SampleIDJob = self.addExtractSampleIDJob(workflow=workflow, outputDirPrefix=outputDirPrefix, \ passingData=passingData, transferOutput=transferOutput, \ pop_tax_id_ls_str=self.pop1_tax_id_ls, pop_site_id_ls_str=self.pop1_site_id_ls, \ pop_country_id_ls_str=self.pop1_country_id_ls, popHeader=self.pop1Header,\ pop_sampleSize=self.pop1_sampleSize, returnData=returnData) passingData.extractPop1SampleIDJob = extractPop1SampleIDJob #ExtractSamplesFromVCF for the 2nd population extractPop2SampleIDJob = self.addExtractSampleIDJob(workflow=workflow, outputDirPrefix=outputDirPrefix, \ passingData=passingData, transferOutput=transferOutput, \ pop_tax_id_ls_str=self.pop2_tax_id_ls, pop_site_id_ls_str=self.pop2_site_id_ls, \ pop_country_id_ls_str=self.pop2_country_id_ls, popHeader=self.pop2Header,\ pop_sampleSize=self.pop2_sampleSize, returnData=returnData) passingData.extractPop2SampleIDJob = extractPop2SampleIDJob return returnData
def registerCustomExecutables(self, workflow=None): """ 2011-11-28 """ AbstractVervetWorkflow.registerCustomExecutables(self, workflow=workflow) AbstractAlignmentAndVCFWorkflow.registerCustomExecutables(self, workflow=workflow) if workflow is None: workflow = self namespace = workflow.namespace version = workflow.version operatingSystem = workflow.operatingSystem architecture = workflow.architecture clusters_size = workflow.clusters_size site_handler = workflow.site_handler vervetSrcPath = self.vervetSrcPath #2012.8.7 each cell is a tuple of (executable, clusterSizeMultipler (0 if u do not need clustering) executableClusterSizeMultiplierList = [] self.addExecutableAndAssignProperClusterSize(executableClusterSizeMultiplierList, defaultClustersSize=self.clusters_size)
def extra__init__(self): """ 2013.2.14 """ AbstractVervetWorkflow.extra__init__(self) AbstractAlignmentAndVCFWorkflow.extra__init__(self)
