def test_composite(self):
il23 = NamedComplexAbundance(namespace='GO',
name='interleukin-23 complex')
il6 = Protein(namespace='HGNC', name='IL6')
node_data = CompositeAbundance([il23, il6])
self.graph.add_node_from_data(node_data)
self.assertIn(node_data, self.graph)
self.assertEqual(3, self.graph.number_of_nodes())
self.assertIn(il6,
self.graph,
msg='Nodes:\n'.format('\n'.join(map(str, self.graph))))
self.assertIn(il23, self.graph)
self.assertEqual(2, self.graph.number_of_edges())
self.assertIn(node_data, self.graph[il6])
edges = list(self.graph[il6][node_data].values())
self.assertEqual(1, len(edges))
data = edges[0]
self.assertEqual(PART_OF, data[RELATION])
self.assertIn(node_data, self.graph[il23])
edges = list(self.graph[il23][node_data].values())
self.assertEqual(1, len(edges))
data = edges[0]
self.assertEqual(PART_OF, data[RELATION])
def test_list_abundance_has_contents(self):
"""Test that the construction of list abundance doesn't have empty lists."""
with self.assertRaises(ListAbundanceEmptyException):
ComplexAbundance([])
with self.assertRaises(ListAbundanceEmptyException):
CompositeAbundance([])
def test_composite(self, mock):
interleukin_23_complex = NamedComplexAbundance(
'GO', 'interleukin-23 complex')
il6 = hgnc(name='IL6')
interleukin_23_and_il6 = CompositeAbundance(
[interleukin_23_complex, il6])
self._help_reconstitute(interleukin_23_and_il6, 3, 2)
def test_remove_isolated_list_abundances(self):
"""Test removing isolated list abundances."""
g = BELGraph()
p1, p2 = [Protein('HGNC', n()) for _ in range(2)]
node = CompositeAbundance([p1, p2])
g.add_node_from_data(node)
self.assertEqual(3, g.number_of_nodes())
remove_isolated_list_abundances(g)
self.assertEqual(2, g.number_of_nodes())
self.assertIn(p1, g)
self.assertIn(p2, g)
def test_composite_abundance(self):
node = CompositeAbundance(members=[
Protein(namespace='HGNC', name='FOS'),
Protein(namespace='HGNC', name='JUN')
])
self.assertEqual('composite(p(HGNC:FOS), p(HGNC:JUN))', str(node))
akt1_rna,
Rna('HGNC', 'AKT1', variants=[Hgvs('c.1521_1523delCTT'), Hgvs('p.Phe508del')]),
Gene('HGNC', 'NCF1'),
ComplexAbundance([
Gene('HGNC', 'NCF1'),
Protein('HGNC', 'HBP1')
]),
Protein('HGNC', 'HBP1'),
ComplexAbundance([Protein('HGNC', 'FOS'), Protein('HGNC', 'JUN')]),
Protein('HGNC', 'FOS'),
Protein('HGNC', 'JUN'),
Rna('HGNC', 'CFTR', variants=Hgvs('r.1521_1523delcuu')),
Rna('HGNC', 'CFTR'),
Rna('HGNC', 'CFTR', variants=Hgvs('r.1653_1655delcuu')),
CompositeAbundance([
interleukin_23_complex,
il6
]),
il6,
BiologicalProcess('GO', 'cell cycle arrest'),
hydrogen_peroxide,
Protein('HGNC', 'CAT'),
Gene('HGNC', 'CAT'),
Protein('HGNC', 'HMGCR'),
BiologicalProcess('GO', 'cholesterol biosynthetic process'),
Gene('HGNC', 'APP', variants=Hgvs('c.275341G>C')),
Gene('HGNC', 'APP'),
Pathology('MESHD', 'Alzheimer Disease'),
ComplexAbundance([Protein('HGNC', 'F3'), Protein('HGNC', 'F7')]),
Protein('HGNC', 'F3'),
Protein('HGNC', 'F7'),
Protein('HGNC', 'F9'),
def test_empty_composite(self):
"""Test that an empty complex causes a failure."""
with self.assertRaises(ValueError):
CompositeAbundance(members=[])
Rna('HGNC',
'AKT1',
variants=[Hgvs('c.1521_1523delCTT'),
Hgvs('p.Phe508del')]),
Gene('HGNC', 'NCF1'),
ComplexAbundance([Gene('HGNC', 'NCF1'),
Protein('HGNC', 'HBP1')]),
Protein('HGNC', 'HBP1'),
ComplexAbundance([Protein('HGNC', 'FOS'),
Protein('HGNC', 'JUN')]),
Protein('HGNC', 'FOS'),
Protein('HGNC', 'JUN'),
Rna('HGNC', 'CFTR', variants=Hgvs('r.1521_1523delcuu')),
Rna('HGNC', 'CFTR'),
Rna('HGNC', 'CFTR', variants=Hgvs('r.1653_1655delcuu')),
CompositeAbundance([interleukin_23_complex, il6]), il6,
BiologicalProcess('GO', 'cell cycle arrest'), hydrogen_peroxide,
Protein('HGNC', 'CAT'),
Gene('HGNC', 'CAT'),
Protein('HGNC', 'HMGCR'),
BiologicalProcess('GO', 'cholesterol biosynthetic process'),
Gene('HGNC', 'APP', variants=Hgvs('c.275341G>C')),
Gene('HGNC', 'APP'),
Pathology('MESHD', 'Alzheimer Disease'),
ComplexAbundance([Protein('HGNC', 'F3'),
Protein('HGNC', 'F7')]),
Protein('HGNC', 'F3'),
Protein('HGNC', 'F7'),
Protein('HGNC', 'F9'),
Protein('HGNC', 'GSK3B', variants=ProteinModification('Ph', 'Ser', 9)),
Protein('HGNC', 'GSK3B'),