def compute(self, timeout): """Filter pathways.""" pf = PathFilter(pathfile=self.pathfile, sinkfile=self.sinkfile, filter_bootstraps=True, filter_inconsistentsubstrates=True, onlyPathsStartingBy=self.onlyPathsStartingBy, notPathsStartingBy=self.notPathsStartingBy) pf.GetPathwaysFromFile() pf.GetSinkCompoundsFromFile() pf.FilterOutPathways() pf.RewritePathFile()