def test_parse_multiple_functional_elements(self):
"""Test that functional elements rows consisting of multiple functional elements can be parsed."""
functional_elements = [('--', ''), ('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('RQ', '0'),
('EV', 'IPR017545; TIGR03114; sufficient;'),
('TG', 'GO:0043571;'),
('ID', 'Yolo subtype specific proteins'),
('RQ', '1'), ('EV', 'IPR017546; TIGR03115;'),
('TG', 'GO:0043571;')]
parsed_functional_elements = parse_functional_elements(
functional_elements)
functional_element_one = parsed_functional_elements[0]
functional_element_two = parsed_functional_elements[1]
self.assertEqual(len(parsed_functional_elements), 2)
evidence_one = functional_element_one.evidence[0]
evidence_two = functional_element_two.evidence[0]
self.assertEqual(evidence_one.evidence_identifiers,
['IPR017545', 'TIGR03114'])
self.assertEqual(evidence_two.evidence_identifiers,
['IPR017546', 'TIGR03115'])
def test_assign_functional_element_none_sufficient_all_not_present(self):
"""Test assignment of a functional element when no sufficient identifiers and none present."""
test_cache = AssignmentCache(interpro_member_database_identifiers=[
'TIGR03115', 'TIGR03118', 'TIGR03121'
])
functional_element = [
('--', ''),
('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('RQ', '0'),
('EV', 'IPR017545; TIGR03114;'), # NO
('EV', 'IPR017547; TIGR03117;'), # NO
('TG', 'GO:0043571;'),
('EV', 'IPR017552; TIGR03120;'), # NO
('TG', 'GO:0043573;')
]
parsed_functional_element = parse_functional_elements(
functional_element)[0]
assignment = assign_functional_element(test_cache,
parsed_functional_element)
self.assertEqual(assignment, 'NO')
def test_assign_functional_element_all_identifiers(self):
"""Test assignment of a functional element when all evidence markers are present."""
test_cache = AssignmentCache(interpro_member_database_identifiers=[
'TIGR03114', 'TIGR03117', 'TIGR03120'
])
functional_element = [
('--', ''),
('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('RQ', '0'),
('EV', 'IPR017545; TIGR03114; sufficient;'), # Yes
('EV', 'IPR017547; TIGR03117;'), # Yes
('TG', 'GO:0043571;'),
('EV', 'IPR017552; TIGR03120;'), # Yes
('TG', 'GO:0043573;')
]
parsed_functional_element = parse_functional_elements(
functional_element)[0]
assignment = assign_functional_element(test_cache,
parsed_functional_element)
self.assertEqual(assignment, 'YES')
def test_parse_missing_rows(self):
"""Test that functional elements can be parsed if they are missing non-essential rows."""
functional_element = [('--', ''), ('SN', '2'),
('ID', 'Apern subtype specific proteins')]
parsed_functional_elements = parse_functional_elements(
functional_element)
second_functional_element = parsed_functional_elements[0]
self.assertEqual(second_functional_element.required, False)
self.assertEqual(second_functional_element.evidence, [])
def test_parse_functional_element(self):
"""Test that functional element rows can be parsed."""
functional_element = [('ID', 'Aferr subtype specific proteins'),
('DN', 'Crispy Proteins'), ('RQ', '0'),
('EV', 'IPR017545; TIGR03114; sufficient;'),
('TG', 'GO:0043571; GO:0043579;')]
parsed_functional_element = parse_functional_elements(
functional_element)
self.assertEqual(len(parsed_functional_element), 1)
first_functional_element = parsed_functional_element[0]
self.assertEqual(first_functional_element.id,
'Aferr subtype specific proteins')
self.assertEqual(first_functional_element.name, 'Crispy Proteins')
self.assertEqual(first_functional_element.required, False)
self.assertEqual(len(first_functional_element.evidence), 1)