def test_1(self):
graph = BELGraph()
u = protein('HGNC', name='U')
v = protein('HGNC', name='V')
w = protein('HGNC', name='W')
graph.add_qualified_edge(u,
v,
relation=INCREASES,
evidence='',
citation='',
annotations={
'A': {'1', '2'},
'B': {'X'}
})
graph.add_qualified_edge(u,
w,
relation=INCREASES,
evidence='',
citation='',
annotations={
'A': {'1', '3'},
'C': {'a'}
})
graph.add_qualified_edge(
w,
v,
relation=INCREASES,
evidence='',
citation='',
)
x = dict(Counter(iter_annotation_value_pairs(graph)))
self.assertEqual(
{
('A', '1'): 2,
('A', '2'): 1,
('A', '3'): 1,
('B', 'X'): 1,
('C', 'a'): 1,
}, x)
y = Counter(iter_annotation_values(graph, 'A'))
self.assertEqual(x['A', '1'] + x['A', '2'] + x['A', '3'],
sum(y.values()))
y = Counter(iter_annotation_values(graph, 'B'))
self.assertEqual(x['B', 'X'], sum(y.values()))
y = Counter(iter_annotation_values(graph, 'C'))
self.assertEqual(x['C', 'a'], sum(y.values()))
def test_1(self):
"""Test iterating over annotation/value pairs."""
graph = BELGraph()
u = protein('HGNC', name='U')
v = protein('HGNC', name='V')
w = protein('HGNC', name='W')
graph.add_increases(u,
v,
evidence=n(),
citation=n(),
annotations={
'A': {'1', '2'},
'B': {'X'}
})
graph.add_increases(u,
w,
evidence=n(),
citation=n(),
annotations={
'A': {'1', '3'},
'C': {'a'}
})
graph.add_increases(
w,
v,
evidence=n(),
citation=n(),
)
x = dict(Counter(iter_annotation_value_pairs(graph)))
self.assertEqual(
{
('A', '1'): 2,
('A', '2'): 1,
('A', '3'): 1,
('B', 'X'): 1,
('C', 'a'): 1,
}, x)
y = Counter(iter_annotation_values(graph, 'A'))
self.assertEqual(x['A', '1'] + x['A', '2'] + x['A', '3'],
sum(y.values()))
y = Counter(iter_annotation_values(graph, 'B'))
self.assertEqual(x['B', 'X'], sum(y.values()))
y = Counter(iter_annotation_values(graph, 'C'))
self.assertEqual(x['C', 'a'], sum(y.values()))
def get_annotation_values(graph, annotation):
"""Get all values for the given annotation
:param pybel.BELGraph graph: A BEL graph
:param str annotation: The annotation to summarize
:return: A set of all annotation values
:rtype: set[str]
"""
return set(iter_annotation_values(graph, annotation))
def count_annotation_values(graph, annotation):
"""Counts in how many edges each annotation appears in a graph
:param pybel.BELGraph graph: A BEL graph
:param str annotation: The annotation to count
:return: A Counter from {annotation value: frequency}
:rtype: collections.Counter
"""
return Counter(iter_annotation_values(graph, annotation))