def bootstrap_assignments(assignment_cache, genome_properties_tree):
"""
Recursively fills in assignments for all genome properties in the genome properties tree based of existing cached
assignments and InterPro member database identifiers.
:param assignment_cache: A cache containing step and property assignments and InterPro member database matches.
:param genome_properties_tree:
:return:
"""
# Bootstrap the other assignments from the leaf assignments.
assign_genome_property(assignment_cache, genome_properties_tree.root)
return assignment_cache
def test_genome_property_assignment_two_required_all_present(self):
"""Test assignment of genome properties when two markers are required and all are present."""
test_cache = AssignmentCache(interpro_member_database_identifiers=[
'TIGR03564', 'TIGR03567', 'TIGR03568'
])
property_rows = [
('AC', 'GenProp0089'),
('DE', 'Coenzyme F420 utilization'),
('TP', 'GUILD'),
('--', ''),
('SN', '1'),
('ID', 'LLM-family F420-associated subfamilies'),
('RQ', '1'),
('EV', 'IPR019910; TIGR03564; sufficient;'), # YES
('--', ''),
('SN', '2'),
('ID', 'LLM-family F420-associated subfamilies'),
('RQ', '1'),
('EV', 'IPR019910; TIGR03567; sufficient;'), # YES
('--', ''),
('SN', '3'),
('ID', 'LLM-family F420-associated subfamilies'),
('RQ', '0'),
('EV', 'IPR019910; TIGR03568; sufficient;') # YES
]
test_property = parse_genome_property(property_rows)
test_property.threshold = 0
assignment = assign_genome_property(test_cache, test_property)
self.assertEqual(assignment, 'YES')
def test_genome_property_assignment_two_required_three_absent(self):
"""Test assignment of genome properties when two markers are required and none are present."""
test_cache = AssignmentCache()
property_rows = [
('AC', 'GenProp0089'),
('DE', 'Coenzyme F420 utilization'),
('TP', 'GUILD'),
('--', ''),
('SN', '1'),
('ID', 'LLM-family F420-associated subfamilies'),
('RQ', '1'),
('EV', 'IPR019910; TIGR03564; sufficient;'), # NO
('--', ''),
('SN', '2'),
('ID', 'LLM-family F420-associated subfamilies'),
('RQ', '1'),
('EV', 'IPR019910; TIGR03567; sufficient;'), # NO
('--', ''),
('SN', '3'),
('ID', 'LLM-family F420-associated subfamilies'),
('RQ', '0'),
('EV', 'IPR019910; TIGR03568; sufficient;') # NO
]
test_property = parse_genome_property(property_rows)
test_property.threshold = 0
assignment = assign_genome_property(test_cache, test_property)
self.assertEqual(assignment, 'NO')
def test_genome_property_assignment_non_required_none_present(self):
"""Test assignment of genome properties when no markers are present and none are required."""
test_cache = AssignmentCache()
test_property = self.tree.root
assignment = assign_genome_property(test_cache, test_property)
self.assertEqual(assignment, 'NO')
def test_genome_property_assignment_non_required_one_present(self):
"""Test assignment of a genome property when one marker is present but none are required."""
test_cache = AssignmentCache(
interpro_member_database_identifiers=['TIGR03565'])
test_property = self.tree.root
assignment = assign_genome_property(test_cache, test_property)
self.assertEqual(assignment, 'PARTIAL')