def test_import_causal(self): """Check a directly increases.""" bel_graph = BELGraph() bel_graph.add_directly_increases(A, B, citation=TEST_CITATION, evidence=TEST_EVIDENCE) bel_graph.add_directly_decreases(B, C, citation=TEST_CITATION, evidence=TEST_EVIDENCE) bel_graph.add_negative_correlation(A, C, citation=TEST_CITATION, evidence=TEST_EVIDENCE) bel_graph.add_association(A, D, citation=TEST_CITATION, evidence=TEST_EVIDENCE) expected = NxMixedGraph.from_edges( directed=[ ('A', 'B'), ('B', 'C'), ], undirected=[ ('A', 'C'), ], ) self.nxmg_equal(expected, bel_to_nxmg(bel_graph, include_associations=False)) expected = NxMixedGraph.from_edges( directed=[ ('A', 'B'), ('B', 'C'), ], undirected=[ ('A', 'C'), ('A', 'D'), ], ) self.nxmg_equal(expected, bel_to_nxmg(bel_graph, include_associations=True))
def test_gap(): sos = protein(name='RASA1', namespace='HGNC') kras = protein(name='KRAS', namespace='HGNC') g = BELGraph() g.add_directly_decreases(sos, kras, subject_modifier=activity(name='activity'), object_modifier=activity(name='gtp'), evidence="Some evidence.", citation='123456') pbp = bel.process_pybel_graph(g) assert pbp.statements assert len(pbp.statements) == 1 stmt = pbp.statements[0] assert isinstance(stmt, Gap) assert stmt.gap.name == 'RASA1' assert stmt.ras.name == 'KRAS' assert stmt.gap.activity.activity_type == 'activity' assert stmt.gap.activity.is_active is True assert stmt.ras.activity is None assert len(pbp.statements[0].evidence) == 1
def _add_to_graph(self, graph: BELGraph, source: pybel.dsl.MicroRna, target: pybel.dsl.Rna) -> str: """Add this edge to the BEL graph and return the ket for that edge.""" return graph.add_directly_decreases( source, target, evidence=str(self.support), citation=str(self.reference), annotations={ 'Experiment': str(self.experiment), 'SupportType': str(self.support), } )
def test_convert_dephosphorylates(self): """Test the conversion of a BEL statement like ``act(p(X)) -| p(Y, pmod(Ph)).""" bel_graph = BELGraph() bel_graph.add_directly_decreases( cdk5, p_tau, evidence=n(), citation=n(), subject_modifier=activity('kin'), ) r_edge = 0 expected_reified_graph = self.help_make_simple_expected_graph( cdk5, p_tau, PHOSPHORYLATES, r_edge, self.help_causal_decreases, ) reified_graph = reify_bel_graph(bel_graph) self.help_test_graphs_equal(expected_reified_graph, reified_graph)