Exemplo n.º 1
0
	def createDumbAssembly(self, falsehood, pval, minlen, minsite):
		vital_params=VitalParameters(falsehood[0], falsehood[1], pval, minlen, minsite)
		vital_params.blocks=self.input_file_blocks

		assembly=Assembly(self.workspace, vital_params)
		self.assemblies.add(assembly)
		self.pairwise_alignments.add(assembly.pairwise_alignment)
		self.splits.add(assembly.split)
		self.sorts.add(assembly.sort)

		if self.input_file_blocks is None:
			self.input_file_blocks=assembly.split.total_job_count
Exemplo n.º 2
0
	def generateFromStepDir(step_dir, blocks=None):
		match_result=re.match("comparison_([^_]+)_([\d\.]+)_([\d\.]+)_([\d\.e-]+)_([\d]+)_([\d]+)_([^/]+)", step_dir)

		work_dir=os.getcwd()
		input_file=match_result.group(1)
		workspace=Workspace(work_dir, input_file)

		fp=match_result.group(2)
		fn=match_result.group(3)
		pval=match_result.group(4)
		minlen=match_result.group(5)
		minsites=match_result.group(6)
		vital_parameters=VitalParameters(fp, fn, pval, minlen, minsites)
		vital_parameters.blocks=blocks

		merge=Merge(workspace, vital_parameters)

		ref_file=match_result.group(7)

		return ReferenceAlignment(workspace, merge, ref_file)