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()
