def append_relations_graph(df: pd.DataFrame, graph: BELGraph):
"""Append FamPlex relations to the graph."""
graph.namespace_url.update(NAMESPACES)
for index, (ns1, n1, rel, ns2, n2) in df.iterrows():
if ns1 == "UP":
continue
sub = protein(ns1, n1)
if rel == 'isa':
obj = protein(ns2, n2)
graph.add_is_a(sub, obj)
else: # partof
obj = named_complex_abundance(ns2, n2)
graph.add_has_member(obj, sub)
def test_component_list(self):
s = 'complex(SCOMP:"C1 Complex") hasComponents list(p(HGNC:C1QB), p(HGNC:C1S))'
result = self.parser.relation.parseString(s)
expected_result_list = [[COMPLEX, 'SCOMP', 'C1 Complex'],
'hasComponents',
[[PROTEIN, 'HGNC', 'C1QB'],
[PROTEIN, 'HGNC', 'C1S']]]
self.assertEqual(expected_result_list, result.asList())
sub = named_complex_abundance('SCOMP', 'C1 Complex')
self.assert_has_node(sub)
child_1 = hgnc('C1QB')
self.assert_has_node(child_1)
self.assert_has_edge(sub, child_1, **{RELATION: HAS_COMPONENT})
child_2 = hgnc('C1S')
self.assert_has_node(child_2)
self.assert_has_edge(sub, child_2, **{RELATION: HAS_COMPONENT})
def test_component_list(self):
s = 'complex(FPLX:C1) hasComponents list(p(HGNC:C1QB), p(HGNC:C1S))'
result = self.parser.relation.parseString(s)
expected_result_list = [[COMPLEX, ['FPLX', 'C1']], 'hasComponents',
[
[PROTEIN, ['HGNC', 'C1QB']],
[PROTEIN, ['HGNC', 'C1S']],
]]
self.assertEqual(expected_result_list, result.asList())
sub = named_complex_abundance('FPLX', 'C1')
self.assert_has_node(sub)
child_1 = hgnc(name='C1QB')
self.assert_has_node(child_1)
self.assert_has_edge(child_1, sub, **{RELATION: PART_OF})
child_2 = hgnc(name='C1S')
self.assert_has_node(child_2)
self.assert_has_edge(child_2, sub, **{RELATION: PART_OF})
example_graph.namespace_url['HGNC'] = ''
example_graph.namespace_pattern['DBSNP'] = r'^rs\d+$'
example_graph.annotation_url['Species'] = ''
example_graph.annotation_pattern['Number'] = r'^\d+$'
example_graph.annotation_list['Confidence'] = {'High', 'Low'}
ptk2 = protein(namespace='HGNC', name='PTK2', variants=[pmod('Ph', 'Tyr', 925)])
mapk1 = protein(namespace='HGNC', name='MAPK1')
mapk3 = protein(namespace='HGNC', name='MAPK3')
grb2 = protein(namespace='HGNC', name='GRB2')
sos1 = protein(namespace='HGNC', name='SOS1')
ptk2_rgb2_sos1 = complex_abundance([mapk1, grb2, sos1])
ras_family = protein(namespace='SFAM', name='RAS Family')
pi3k_complex = named_complex_abundance(namespace='SFAM', name='p85/p110 PI3Kinase Complex')
kinase_activity = activity('kin')
catalytic_activity = activity('cat')
gtp_activity = activity('gtp')
c1 = '10446041'
e1 = "FAK also combines with, and may activate, phosphoinositide 3-OH kinase (PI 3-kinase), either directly or " \
"through the Src kinase (13). Finally, there is evidence that Src phosphorylates FAK at Tyr925, creating a" \
" binding site for the complex of the adapter Grb2 and Ras guanosine 5'-triphosphate exchange factor mSOS (10)." \
" These interactions link FAK to signaling pathways that modify the cytoskeleton and activate mitogen-activated" \
" protein kinase (MAPK) cascades (Fig. 3A)."
e1 = str(hash(e1))
"""
def test_named_complex_abundance(self):
node = named_complex_abundance(namespace='SCOMP',
name='Calcineurin Complex')
self.assertEqual('complex(SCOMP:"Calcineurin Complex")', str(node))
