コード例 #1
0
	def registerCustomExecutables(self, workflow):
		"""
		2011-11-28
		"""
		FilterVCFPipeline.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
コード例 #2
0
	def __init__(self,  **keywords):
		"""
		"""
		FilterVCFPipeline.__init__(self, **keywords)
		self.inputDir = os.path.abspath(self.inputDir)
		
		
		listArgumentName_data_type_ls = [('depthFoldChangeLs', int), ("minDepthPerGenotypeLs", int), \
								("minMACLs", int), ("minMAFLs", float), ("maxSNPMissingRateLs", float)]
		listArgumentName2hasContent = self.processListArguments(listArgumentName_data_type_ls, emptyContent=[None])
		if listArgumentName2hasContent['depthFoldChangeLs'] and not self.alnStatForFilterFname:
			sys.stderr.write("Error: alnStatForFilterFname (%s) is nothing while depthFoldChangeLs=%s.\n"%\
							(self.alnStatForFilterFname, repr(self.depthFoldChangeLs)))
			sys.exit(3)
コード例 #3
0
	def __init__(self,  **keywords):
		"""
		"""
		FilterVCFPipeline.__init__(self, **keywords)