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)
