def test_to_networkx(self):
g = terms_to_graph(self.terms_diam)
na = g.to_networkx({"GO:0050896" : ["X1", "X2"]})
self.assertEqual(["GO:0030534", "GO:0045471"], na.successors("GO:0048149"))
self.assertEqual(["GO:0050896"], na.successors("GO:0030534"))
self.assertEqual(["GO:0050896"], na.successors("GO:0045471"))
self.assertEqual(["X1", "X2"], na.node["GO:0050896"]["annotated_genes"])
def test_get_parents_cycle(self):
g = terms_to_graph(self.terms_cycle)
self.assertEqual(set(['GO:0030534', 'GO:0050896', 'GO:0005374',
'GO:0048149', 'GO:0045471']),
g.get_ancestors("GO:0048149"))
self.assertEqual([['GO:0048149', 'GO:0005374']], g.cycles)
def test_get_parents_cycle(self):
g = terms_to_graph(self.terms_cycle)
self.assertEqual(set(['GO:0030534', 'GO:0050896', 'GO:0005374',
'GO:0048149', 'GO:0045471']),
g.get_ancestors("GO:0048149"))
self.assertEqual([['GO:0048149', 'GO:0005374']], g.cycles)
def test_to_networkx(self):
g = terms_to_graph(self.terms_diam)
na = g.to_networkx({"GO:0050896": ["X1", "X2"]})
self.assertEqual(["GO:0030534", "GO:0045471"],
na.successors("GO:0048149"))
self.assertEqual(["GO:0050896"], na.successors("GO:0030534"))
self.assertEqual(["GO:0050896"], na.successors("GO:0045471"))
self.assertEqual(["X1", "X2"],
na.node["GO:0050896"]["annotated_genes"])
def test_to_networkx(self):
try:
import networkx as nx
except ImportError:
print("Skipping test. To use this functionality you need to have networkx installed.", file=sys.stderr)
else:
g = terms_to_graph(self.terms_diam)
na = g.to_networkx({"GO:0050896" : ["X1", "X2"]})
self.assertEqual(["GO:0030534", "GO:0045471"], na.successors("GO:0048149"))
self.assertEqual(["GO:0050896"], na.successors("GO:0030534"))
self.assertEqual(["GO:0050896"], na.successors("GO:0045471"))
self.assertEqual(["X1", "X2"], na.node["GO:0050896"]["annotated_genes"])
def test_no_typedef(self):
with self.assertRaises(ValueError):
terms_to_graph(self.terms_cycle_no)
def test_bad_rel(self):
with self.assertRaises(ValueError):
terms_to_graph(self.terms_bad_rel)
def test_get_ancestors(self):
g = terms_to_graph(self.terms_diam)
self.assertEqual(set(["GO:0030534", "GO:0045471", "GO:0050896"]),
g.get_ancestors("GO:0048149"))
self.assertEqual(set(["GO:0050896"]), g.get_ancestors("GO:0030534"))
def test_get_term(self):
g = terms_to_graph(self.terms_diam)
self.assertEqual("GO:0045471", g.get_term("GO:0045471").id)
def test_no_typedef(self):
with self.assertRaises(ValueError):
terms_to_graph(self.terms_cycle_no)
def test_bad_rel(self):
with self.assertRaises(ValueError):
terms_to_graph(self.terms_bad_rel)
def test_get_ancestors(self):
g = terms_to_graph(self.terms_diam)
self.assertEqual(set(["GO:0030534", "GO:0045471", "GO:0050896"]),
g.get_ancestors("GO:0048149"))
self.assertEqual(set(["GO:0050896"]), g.get_ancestors("GO:0030534"))
def test_get_term(self):
g = terms_to_graph(self.terms_diam)
self.assertEqual("GO:0045471", g.get_term("GO:0045471").id)