def test_names_sialic(self):
"""Test getting and counting names by namespace."""
result = {
'CD33': 3, # once as reference, once in complex, and once as variant
'TYROBP': 1,
'SYK': 1,
'PTPN6': 1,
'PTPN11': 1,
'TREM2': 1,
}
self.assertEqual(set(result), get_names_by_namespace(sialic_acid_graph, 'HGNC'))
self.assertEqual(result, dict(count_names_by_namespace(sialic_acid_graph, 'HGNC')))
def test_summarize_sialic(self):
"""Test getting and counting namespaces' contents on the sialic acid graph."""
namespace_result = {
'hgnc': 8,
'chebi': 2,
'bel': 3,
}
self.assertEqual(set(namespace_result),
get_namespaces(sialic_acid_graph))
self.assertEqual(Counter(namespace_result),
count_namespaces(sialic_acid_graph))
hgnc_result = {
'CD33':
3, # once as reference, once in complex, and once as variant
'TYROBP': 1,
'SYK': 1,
'PTPN6': 1,
'PTPN11': 1,
'TREM2': 1,
}
chebi_result = {
'sialic acid': 2,
}
names = get_names(sialic_acid_graph)
self.assertEqual(set(namespace_result), set(names))
self.assertEqual(set(hgnc_result), names['hgnc'])
self.assertEqual(set(chebi_result), names['chebi'])
self.assertEqual(set(hgnc_result),
get_names_by_namespace(sialic_acid_graph, 'hgnc'))
self.assertEqual(set(chebi_result),
get_names_by_namespace(sialic_acid_graph, 'chebi'))
self.assertEqual(
hgnc_result,
dict(count_names_by_namespace(sialic_acid_graph, 'hgnc')))
self.assertEqual(
chebi_result,
dict(count_names_by_namespace(sialic_acid_graph, 'chebi')))
def test_names_sialic(self):
result = {
'CD33': 2,
'TYROBP': 1,
'SYK': 1,
'PTPN6': 1,
'PTPN11': 1,
'TREM2': 1,
}
self.assertEqual(set(result),
get_names_by_namespace(sialic_acid_graph, 'HGNC'))
self.assertEqual(result,
count_names_by_namespace(sialic_acid_graph, 'HGNC'))
def test_names_sialic(self):
"""Test getting and counting names by namespace."""
result = {
'CD33': 2,
'TYROBP': 1,
'SYK': 1,
'PTPN6': 1,
'PTPN11': 1,
'TREM2': 1,
}
self.assertEqual(set(result),
get_names_by_namespace(sialic_acid_graph, 'HGNC'))
self.assertEqual(Counter(result),
count_names_by_namespace(sialic_acid_graph, 'HGNC'))
def test_names_fusions(self):
"""Test that names inside fusions are still found by the iterator."""
graph = BELGraph()
graph.namespace_url['HGNC'] = 'http://dummy'
node = protein_fusion(partner_5p=protein(name='A', namespace='HGNC'),
range_5p=fusion_range('p', 1, 15),
partner_3p=protein(name='B', namespace='HGNC'),
range_3p=fusion_range('p', 1, 100))
graph.add_node_from_data(node)
result = {
'A': 1,
'B': 1,
}
self.assertEqual(set(result), get_names_by_namespace(graph, 'HGNC'))
self.assertEqual(result, count_names_by_namespace(graph, 'HGNC'))
def test_count_names_raise(self):
"""Test that an index error is raised when trying to count a namespace that isn't present."""
with self.assertRaises(IndexError):
count_names_by_namespace(sialic_acid_graph, 'NOPE')
def test_count_names_raise(self):
with self.assertRaises(IndexError):
count_names_by_namespace(sialic_acid_graph, 'NOPE')