def test_neighborhoods(self):
"""Test expansion on the neighborhood of given nodes.
The edge between PTPN6/CD33ph should not be added.
"""
graph = BELGraph()
graph.add_node_from_data(cd33)
graph.add_node_from_data(syk)
self.assertEqual(2, graph.number_of_nodes())
_sialic_acid_graph = sialic_acid_graph.copy()
expand_nodes_neighborhoods(universe=_sialic_acid_graph,
graph=graph,
nodes=[cd33, syk])
self.assertNotIn(shp1, graph[cd33_phosphorylated])
self.assertNotIn(shp2, graph[cd33_phosphorylated])
self.assertEqual(9,
graph.number_of_nodes(),
msg='wrong number of nodes: {}'.format(list(graph)))
self.assertEqual(8,
graph.number_of_edges(),
msg='wrong number of edges')
self.assertIn(sialic_acid, graph)
self.assertIn(sialic_acid_cd33_complex, graph)
self.assertIn(cd33_phosphorylated, graph)
def test_neighborhood(self):
"""Test expansion around the neighborhood of CD33 in the sialic acid graph given node."""
graph = BELGraph()
graph.add_node_from_data(cd33)
self.assertEqual(1, graph.number_of_nodes())
_sialic_acid_graph = sialic_acid_graph.copy()
expand_node_neighborhood(graph=graph,
universe=_sialic_acid_graph,
node=cd33)
self.assertEqual(
{cd33, sialic_acid, sialic_acid_cd33_complex, cd33_phosphorylated},
set(graph),
)
def test_neighborhood_with_successors(self):
"""Test expansion on the successors of a given node."""
graph = BELGraph()
graph.add_node_from_data(cd33)
graph.add_node_from_data(cd33_phosphorylated)
self.assertEqual(2, graph.number_of_nodes())
_sialic_acid_graph = sialic_acid_graph.copy()
expand_node_successors(universe=_sialic_acid_graph,
graph=graph,
node=cd33)
self.assertEqual(
{sialic_acid_cd33_complex, sialic_acid, cd33_phosphorylated, cd33},
set(graph),
)
def test_neighborhood_with_predecessors(self):
"""Test expansion on the predecessors of a given node."""
graph = BELGraph()
graph.add_node_from_data(cd33)
graph.add_node_from_data(sialic_acid_cd33_complex)
self.assertEqual(3, graph.number_of_nodes())
_sialic_acid_graph = sialic_acid_graph.copy()
expand_node_predecessors(universe=_sialic_acid_graph,
graph=graph,
node=cd33)
self.assertEqual(4, graph.number_of_nodes())
self.assertIn(sialic_acid, graph)
self.assertIn(sialic_acid_cd33_complex, graph)
self.assertIn(cd33_phosphorylated, graph)
def test_seeding_with_pipeline(self):
test_network_1 = self.manager.insert_graph(sialic_acid_graph.copy())
query = Query(network_ids=[test_network_1.id])
query.append_seeding_neighbors([trem2, dap12, shp2])
query.append_pipeline(expand_nodes_neighborhoods, [trem2, dap12, shp2])
result = query.run(self.manager)
self.assertIsNotNone(result, msg='Query returned none')
self.assertIsInstance(result, BELGraph)
self.assertIn(trem2, result)
self.assertIn(dap12, result)
self.assertIn(shp2, result)
self.assertIn(syk, result)
self.assertIn(cd33_phosphorylated, result)
self.assertEqual(5, result.number_of_nodes())
self.assertEqual(4, result.number_of_edges())
def test_query_multiple_networks(self):
egf_network = self.manager.insert_graph(sialic_acid_graph.copy())
sialic_acid_network = self.manager.insert_graph(egf_graph.copy())
query = Query()
query.append_network(egf_network.id)
query.append_network(sialic_acid_network.id)
query.append_seeding_neighbors([syk.as_tuple()])
query.append_pipeline(infer_central_dogma)
result = query.run(self.manager, in_place=False)
self.assertIsNotNone(result, msg='Query returned none')
self.assertIn(shp1.as_tuple(), result)
self.assertIn(shp2.as_tuple(), result)
self.assertIn(trem2.as_tuple(), result)
self.assertIn(dap12.as_tuple(), result)
self.assertEqual(15, result.number_of_nodes())
self.assertEqual(14, result.number_of_edges())
def test_query_multiple_networks(self):
sialic_acid_graph_id = self.manager.insert_graph(sialic_acid_graph.copy()).id
egf_graph_id = self.manager.insert_graph(egf_graph.copy()).id
query = Query()
query.append_network(sialic_acid_graph_id)
query.append_network(egf_graph_id)
query.append_seeding_neighbors([syk])
query.append_pipeline(enrich_protein_and_rna_origins)
result = query.run(self.manager)
self.assertIsNotNone(result, msg='Query returned none')
self.assertIn(shp1, result)
self.assertIn(shp2, result)
self.assertIn(trem2, result)
self.assertIn(dap12, result)
self.assertEqual(15, result.number_of_nodes())
self.assertEqual(14, result.number_of_edges())
def setUp(self):
self.sialic_acid_graph = sialic_acid_graph.copy()
def setUp(self):
self.sialic_acid_graph = sialic_acid_graph.copy()
self.single_reaction_graph = single_reaction_graph.copy()
self.single_composite_graph = single_composite_graph.copy()
self.single_complex_graph = single_complex_graph.copy()