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
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)
