def test_update_matrix_pmods(self):
"""Test updating the matrix with multiple protein modifications."""
sub = protein(namespace='HGNC', name='A', identifier='1')
obj = protein(namespace='HGNC', name='B', identifier='2', variants=[pmod('Ub'), pmod('Ph')])
index = {'A', 'B'}
test_dict = {}
test_matrix = DataFrame(0, index=index, columns=index)
test_dict["activation_ubiquination"] = test_matrix
test_dict["activation_phosphorylation"] = test_matrix
update_spia_matrices(test_dict, sub, obj, {'relation': 'increases'})
self.assertEqual(test_dict["activation_ubiquination"]['A']['B'], 1)
self.assertEqual(test_dict["activation_ubiquination"]['A']['A'], 0)
self.assertEqual(test_dict["activation_ubiquination"]['B']['A'], 0)
self.assertEqual(test_dict["activation_ubiquination"]['B']['B'], 0)
self.assertEqual(test_dict["activation_phosphorylation"]['A']['B'], 1)
self.assertEqual(test_dict["activation_phosphorylation"]['A']['A'], 0)
self.assertEqual(test_dict["activation_phosphorylation"]['B']['A'], 0)
self.assertEqual(test_dict["activation_phosphorylation"]['B']['B'], 0)
def test_update_matrix_inhibition_ubiquination(self):
"""Test updating the matrix with an inhibition ubiquitination."""
sub = protein(namespace='HGNC', name='A', identifier='1')
obj = protein(namespace='HGNC',
name='B',
identifier='2',
variants=[pmod('Ub')])
index = {'A', 'B'}
test_dict = {}
test_matrix = DataFrame(0, index=index, columns=index)
# Initialize matrix correctly
self.assertEqual(test_matrix.values.all(), 0)
test_dict["inhibition_ubiquination"] = test_matrix
update_spia_matrices(test_dict, sub, obj, {'relation': 'decreases'})
self.assertEqual(test_dict["inhibition_ubiquination"]['A']['B'], 1)
self.assertEqual(test_dict["inhibition_ubiquination"]['A']['A'], 0)
self.assertEqual(test_dict["inhibition_ubiquination"]['B']['A'], 0)
self.assertEqual(test_dict["inhibition_ubiquination"]['B']['B'], 0)
def test_update_matrix_inhibition_phosphorylation(self):
"""Test updating the matrix with an inhibition phosphorylation."""
sub = protein(namespace='HGNC', name='A', identifier='1')
obj = protein(namespace='HGNC', name='B', identifier='2', variants=[pmod('Ph')])
index = {'A', 'B'}
test_dict = {}
test_matrix = DataFrame(0, index=index, columns=index)
test_dict["inhibition_phosphorylation"] = test_matrix
update_spia_matrices(test_dict, sub, obj, {'relation': 'decreases'})
self.assertEqual(test_dict["inhibition_phosphorylation"]['A']['B'], 1)
self.assertEqual(test_dict["inhibition_phosphorylation"]['A']['A'], 0)
self.assertEqual(test_dict["inhibition_phosphorylation"]['B']['A'], 0)
self.assertEqual(test_dict["inhibition_phosphorylation"]['B']['B'], 0)
def test_update_matrix_association(self):
"""Test updating the matrix with association."""
sub = protein(namespace='HGNC', name='A', identifier='1')
obj = protein(namespace='HGNC', name='B', identifier='2')
index = {'A', 'B'}
test_dict = {}
test_matrix = DataFrame(0, index=index, columns=index)
test_dict["binding_association"] = test_matrix
update_spia_matrices(test_dict, sub, obj, {'relation': 'association'})
self.assertEqual(test_dict["binding_association"]['A']['B'], 1)
self.assertEqual(test_dict["binding_association"]['A']['A'], 0)
self.assertEqual(test_dict["binding_association"]['B']['A'], 0)
self.assertEqual(test_dict["binding_association"]['B']['B'], 0)