class EnrichmentFinderTest(unittest.TestCase):
def setUp(self):
self.go_graph = OntoIO.read("Ontology/go_test.obo", "obo")
self.assocs = OntoIO.read("Ontology/ga_test.fb", "gaf")
self.ef = TermForTermEnrichmentFinder(self.assocs, self.go_graph)
def test_find_terms_associations(self):
expected = {'GO:0032502': set(['FBgn0010340']),'GO:0005737': set(['FBgn0026615']), 'GO:0045177': set(['FBgn0026615']), 'GO:0032501': set(['FBgn0010340']), 'GO:0044707': set(['FBgn0010340']), 'GO:0044464': set(['FBgn0026615']), 'GO:0005623': set(['FBgn0026615']), 'GO:0005622': set(['FBgn0026615']), 'GO:0005575': set(['FBgn0026615']), 'GO:0008150': set(['FBgn0010340', 'FBgn0026615']), 'GO:0044424': set(['FBgn0026615']), 'GO:0003674': set(['FBgn0026615']), 'GO:0007275': set(['FBgn0010340']), 'GO:0044699': set(['FBgn0010340'])}
self.assertEqual(expected, self.ef._find_terms_associations(['FBgn0010340', 'FBgn0026615']))
def test_parent_child_union(self):
genes = ['FBgn0043467', 'FBgn0010339', 'FBgn0070057', 'FBgn0070052']
ef = ParentChildEnrichmentFinder(self.assocs, self.go_graph)
en = ef.find_enrichment(genes, ['bh_fdr'], 'union')
self.assertEqual(7, len(en.filter_p_val(0.9).entries))
def test_parent_child_intersection(self):
genes = ['FBgn0043467', 'FBgn0010339', 'FBgn0070057', 'FBgn0070052']
ef = ParentChildEnrichmentFinder(self.assocs, self.go_graph)
en = ef.find_enrichment(genes, ['bonferroni'], 'intersection')
self.assertEqual(7, len(en.filter_p_val(0.9).entries))
def test_term_for_term(self):
genes = ['FBgn0043467', 'FBgn0010339', 'FBgn0070057', 'FBgn0070052']
en = self.ef.find_enrichment(genes)
self.assertEqual(24, len(en.filter_p_val(0.9).entries))
def run_term(assocs, go_graph, gene_list, corrections):
from Bio.Ontology import TermForTermEnrichmentFinder
ef = TermForTermEnrichmentFinder(assocs, go_graph)
result = ef.find_enrichment(gene_list, corrections)
return result
def setUp(self):
self.go_graph = OntoIO.read("Ontology/go_test.obo", "obo")
self.assocs = OntoIO.read("Ontology/ga_test.fb", "gaf")
self.ef = TermForTermEnrichmentFinder(self.assocs, self.go_graph)
def run_term(assocs, go_graph, gene_list, corrections):
from Bio.Ontology import TermForTermEnrichmentFinder
ef = TermForTermEnrichmentFinder(assocs, go_graph)
result = ef.find_enrichment(gene_list, corrections)
return result