class TestLabels(unittest.TestCase):
def setUp(self):
self.go = OBO('files/test_data/go.obo')
self.go.populate_annotations(GO_URL, remote_location=True)
self.dsrepair_term = self.go.get_term(DSREPAIR_ID)
lines = open('files/go_neg_slim.txt').readlines()
self.slim_terms = set([l.strip() for l in lines])
def testOntoLabelsNeg(self):
ol = OntoLabels(obo=self.go, slim_terms=self.slim_terms)
(pos, neg) = ol.get_labels(DSREPAIR_ID)
self.assertTrue(len(pos) > 0)
self.assertEqual(pos,set(self.dsrepair_term.get_annotated_genes()))
similar_term = self.go.get_term(DNA_REP_ID).get_annotated_genes()
slim_overlap = self.go.get_ancestors(DNA_REP_ID) & \
self.go.get_ancestors(DSREPAIR_ID) & \
self.slim_terms
self.assertTrue(DNA_METAB in slim_overlap)
self.assertTrue(len(neg & set(similar_term)) == 0)
for dterm in self.go.get_descendents(DNA_METAB):
dgenes = set(self.go.get_term(dterm).get_annotated_genes())
self.assertTrue(len(neg & dgenes) == 0)
for (tissue, stds) in tissue_std_edges.iteritems():
c3 = tissue_std_edges[tissue]['0']
for c3_edge in list(c3):
# Limit negative edges to positive genes
if len(c3_edge & tissue_all_pos) < 2:
c3.remove(c3_edge)
for (tissue, stds) in tissue_std_edges.iteritems():
c1 = tissue_std_edges[tissue]['1']
c1_g = reduce(frozenset.union, c1)
c1_tspc = c1_g - ubiq
c3 = tissue_std_edges[tissue]['0']
c3_g = reduce(frozenset.union, c3)
c3_tspc = c3_g - ubiq
c2 = within_edges_pos - c1
c4 = within_edges_neg - c3
if onto:
for dtissue in onto.get_descendents(tissue):
if dtissue in tissue_std_edges:
c2 -= tissue_std_edges[dtissue]['1']
c4 -= tissue_std_edges[dtissue]['0']
for atissue in onto.get_ancestors(tissue):
if atissue in tissue_std_edges:
c2 -= tissue_std_edges[atissue]['1']
c4 -= tissue_std_edges[atissue]['0']
print tissue, len(c1_tspc), len(c1), len(c2), len(c3), len(c4)