def get_drug_scores(
graph: BELGraph,
dtis: Mapping[str, List[Gene]],
preprocess_graph: bool = True,
) -> Iterable[Tuple[str, str, float]]:
"""Get drug scores for the given graph."""
if preprocess_graph:
logger.info('preprocessing %s', graph)
graph = neurommsig_graph_preprocessor(graph)
logger.info('stratifying %s', graph)
subgraphs = get_subgraphs_by_annotation(graph,
annotation='Subgraph',
sentinel='UNDEFINED')
logger.info('running subgraphs x drugs for %s', graph)
it = itt.product(sorted(subgraphs), sorted(dtis))
it = tqdm(it, total=len(subgraphs) * len(dtis), desc='Calculating scores')
def get_score(s: str, d: str) -> Optional[float]:
"""Get the score for the given subgraph and drug."""
return get_neurommsig_score(subgraphs[s], dtis[d])
for subgraph_name, drug in it:
score = get_score(subgraph_name, drug)
if score is None or score == 0.0:
continue
yield drug, subgraph_name, score
def test_get_subgraphs_by_annotation_with_sentinel(self):
sentinel = n()
subgraphs = get_subgraphs_by_annotation(self.graph, annotation='subgraph', sentinel=sentinel)
self.assertEqual(3, len(subgraphs))
self.assertIn(Entity(namespace='subgraph', identifier='1'), subgraphs)
self.assertIn(Entity(namespace='subgraph', identifier='2'), subgraphs)
self.assertIn(sentinel, subgraphs)
def test_get_subgraphs_by_annotation_with_sentinel(self):
sentinel = n()
subgraphs = get_subgraphs_by_annotation(self.graph,
annotation='subgraph',
sentinel=sentinel)
self.assertEqual(3, len(subgraphs))
self.assertIn('1', subgraphs)
self.assertIn('2', subgraphs)
self.assertIn(sentinel, subgraphs)
def test_get_subgraphs_by_annotation(self):
subgraphs = get_subgraphs_by_annotation(self.graph,
annotation='subgraph')
self.assertEqual(2, len(subgraphs))
self.assertIn('1', subgraphs)
self.assertIn('2', subgraphs)
subgraph_1 = subgraphs['1']
self.assertIsInstance(subgraph_1, BELGraph)
self.assertIn('test', subgraph_1.namespace_url)
self.assertIn('subgraph', subgraph_1.annotation_url)
self.assertIn(a, subgraph_1)
self.assertIn(FUNCTION, subgraph_1.node[a.as_tuple()])
self.assertEqual(PROTEIN, subgraph_1.node[a.as_tuple()][FUNCTION])
self.assertIn(b, subgraph_1)
self.assertIn(c, subgraph_1)
self.assertIn(d, subgraph_1)
self.assertIn(b.as_tuple(), subgraph_1[a.as_tuple()])
self.assertIn(c.as_tuple(), subgraph_1[a.as_tuple()])
self.assertIn(d.as_tuple(), subgraph_1[b.as_tuple()])
self.assertNotIn(d.as_tuple(), subgraph_1[a.as_tuple()])
self.assertNotIn(d.as_tuple(), subgraph_1[c.as_tuple()])
subgraph_2 = subgraphs['2']
self.assertIsInstance(subgraph_2, BELGraph)
self.assertIn('test', subgraph_2.namespace_url)
self.assertIn('subgraph', subgraph_2.annotation_url)
self.assertIn(a, subgraph_2)
self.assertIn(b, subgraph_2)
self.assertNotIn(c, subgraph_2)
self.assertIn(d, subgraph_2)
self.assertIn(b.as_tuple(), subgraph_2[a.as_tuple()])
self.assertNotIn(c.as_tuple(), subgraph_2[a.as_tuple()])
self.assertIn(d.as_tuple(), subgraph_2[b.as_tuple()])
self.assertIn(d.as_tuple(), subgraph_2[a.as_tuple()])
def test_get_subgraphs_by_annotation(self):
subgraphs = get_subgraphs_by_annotation(self.graph,
annotation='subgraph')
self.assertEqual(2, len(subgraphs))
self.assertIn('1', subgraphs)
self.assertIn('2', subgraphs)
subgraph_1 = subgraphs['1']
self.assertIsInstance(subgraph_1, BELGraph)
self.assertIn('test', subgraph_1.namespace_url)
self.assertIn('subgraph', subgraph_1.annotation_url)
self.assertIn(a, subgraph_1)
self.assertIn(b, subgraph_1)
self.assertIn(c, subgraph_1)
self.assertIn(d, subgraph_1)
self.assertIn(b, subgraph_1[a])
self.assertIn(c, subgraph_1[a])
self.assertIn(d, subgraph_1[b])
self.assertNotIn(d, subgraph_1[a])
self.assertNotIn(d, subgraph_1[c])
subgraph_2 = subgraphs['2']
self.assertIsInstance(subgraph_2, BELGraph)
self.assertIn('test', subgraph_2.namespace_url)
self.assertIn('subgraph', subgraph_2.annotation_url)
self.assertIn(a, subgraph_2)
self.assertIn(b, subgraph_2)
self.assertNotIn(c, subgraph_2)
self.assertIn(d, subgraph_2)
self.assertIn(b, subgraph_2[a])
self.assertNotIn(c, subgraph_2[a])
self.assertIn(d, subgraph_2[b])
self.assertIn(d, subgraph_2[a])