def test_parse_multiple_evidences(self):
"""Test that literature reference rows consisting of multiple references can be parsed."""
evidences = [
('--', ''),
('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('RQ', '0'),
('EV', 'IPR017545; TIGR03114; sufficient;'),
('EV', 'IPR017547; TIGR03117;'),
('TG', 'GO:0043571;'),
('EV', 'IPR017552; TIGR03120;'),
('TG', 'GO:0043573;')
]
parsed_evidences = parse_evidences(evidences)
first_evidence = parsed_evidences[0]
second_evidence = parsed_evidences[1]
third_evidence = parsed_evidences[2]
self.assertEqual(len(parsed_evidences), 3)
self.assertEqual(first_evidence.evidence_identifiers, ['IPR017545', 'TIGR03114'])
self.assertEqual(first_evidence.gene_ontology_terms, [])
self.assertEqual(second_evidence.evidence_identifiers, ['IPR017547', 'TIGR03117'])
self.assertEqual(third_evidence.gene_ontology_terms, ['GO:0043573'])
def test_has_genome_property(self):
"""Test that we can determine that an evidence is a genome property."""
evidences = [('--', ''), ('SN', '3'),
('ID', 'Selfish genetic elements'), ('RQ', '0'),
('EV', 'GenProp0066;')]
evidence = parse_evidences(evidences)[0]
self.assertEqual(evidence.has_genome_property, True)
def test_parse_evidence_insufficient(self):
"""Test that the evidence rows can be properly parsed if the evidence is insufficient."""
evidence = [('--', ''), ('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('DN', 'Crispy Proteins'), ('RQ', '1'),
('EV', 'IPR017545; TIGR03114;'), ('TG', 'GO:0043571;')]
parsed_evidence = parse_evidences(evidence)
first_evidence = parsed_evidence[0]
self.assertEqual(first_evidence.sufficient, False)
def test_get_genome_property_identifiers(self):
"""Test that we can determine that an evidence is a genome property."""
evidences = [('--', ''), ('SN', '3'),
('ID', 'Selfish genetic elements'), ('RQ', '0'),
('EV', 'GenProp0066; GenProp0067;')]
evidence = parse_evidences(evidences)[0]
self.assertEqual(evidence.genome_property_identifiers,
['GenProp0066', 'GenProp0067'])
def test_parse_evidence_no_go_terms(self):
"""Test that the evidence rows can be properly parsed if the evidence has no go terms."""
evidence = [
('--', ''),
('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('DN', 'Crispy Proteins'),
('RQ', '1'),
('EV', 'IPR017545; TIGR03114;'),
]
parsed_evidence = parse_evidences(evidence)
first_evidence = parsed_evidence[0]
self.assertEqual(first_evidence.gene_ontology_terms, [])
def test_get_consortium_identifiers(self):
"""Test that we can get the consortium identifiers for an evidence."""
evidence = [
('--', ''),
('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('DN', 'Crispy Proteins'),
('RQ', '0'),
('EV', 'IPR017545; TIGR03114; sufficient;'),
('TG', 'GO:0043571;')
]
evidence = parse_evidences(evidence)[0]
self.assertEqual(evidence.consortium_identifiers, ['TIGR03114'])
def test_assign_evidence_from_no_interpro_identifiers(self):
"""Test we can assign evidence when no InterPro identifiers are in the assignment cache."""
test_cache = AssignmentCache()
evidence = [('--', ''), ('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('DN', 'Crispy Proteins'), ('RQ', '0'),
('EV', 'IPR017545; TIGR03114; sufficient;'),
('TG', 'GO:0043571;')]
evidence = parse_evidences(evidence)[0]
assignment = assign_evidence(test_cache, evidence)
self.assertEqual(assignment, 'NO')
def test_parse_evidence(self):
"""Test that evidence rows can be parsed."""
evidence = [('--', ''), ('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('DN', 'Crispy Proteins'), ('RQ', '0'),
('EV', 'IPR017545; TIGR03114; sufficient;'),
('TG', 'GO:0043571;')]
parsed_evidence = parse_evidences(evidence)
self.assertEqual(len(parsed_evidence), 1)
first_evidence = parsed_evidence[0]
self.assertEqual(first_evidence.evidence_identifiers,
['IPR017545', 'TIGR03114'])
self.assertEqual(first_evidence.gene_ontology_terms, ['GO:0043571'])
self.assertEqual(first_evidence.sufficient, True)
def test_assign_evidence_when_missing_interpro_identifiers(self):
"""Test assign evidence based on InterPro identifiers that are missing from the assignment cache."""
test_cache = AssignmentCache(interpro_member_database_identifiers=[
'TIGR03192', 'TIGR03193', 'TIGR03194'
])
evidence = [('--', ''), ('SN', '1'),
('ID', 'Aferr subtype specific proteins'),
('DN', 'Crispy Proteins'), ('RQ', '0'),
('EV', 'IPR017545; TIGR03114; sufficient;'),
('TG', 'GO:0043571;')]
evidence = parse_evidences(evidence)[0]
assignment = assign_evidence(test_cache, evidence)
self.assertEqual(assignment, 'NO')