def parse_genome_property_longform_file(longform_file):
"""
Parses longform genome properties assignment files.
:param longform_file: A longform genome properties assignment file handle object.
:return: An assignment cache object.
"""
property_id = ''
step_number = ''
assignment_cache = AssignmentCache(sample_name=splitext(basename(longform_file.name))[0])
for line in longform_file:
if 'PROPERTY:' in line:
property_id = line.split(':')[1].strip()
elif 'STEP NUMBER:' in line:
step_number = int(line.split(':')[1].strip())
elif 'RESULT:' in line:
assignment = line.split(':')[1].strip().upper()
if 'STEP' in line:
assignment_cache.cache_step_assignment(property_id, step_number, assignment)
else:
assignment_cache.cache_property_assignment(property_id, assignment)
else:
continue
return assignment_cache
def test_get_identifiers(self):
"""Test that we can get the correct assignment identifiers from the cache."""
test_cache = AssignmentCache()
test_cache.cache_property_assignment('GenProp0067', 'YES')
test_cache.cache_property_assignment('GenProp0092', 'NO')
identifiers = test_cache.genome_property_identifiers
identifiers.sort()
self.assertEqual(identifiers, ['GenProp0067', 'GenProp0092'])
def test_assignment_cache_synchronization(self):
"""Test that the assignment file can be properly synchronized."""
test_cache = AssignmentCache()
test_tree = self.test_tree
test_cache.cache_property_assignment('GenProp0456', 'YES')
test_cache.cache_property_assignment('GenProp0710', 'YES')
sanitized_cache = create_synchronized_assignment_cache(test_cache, test_tree)
self.assertEqual(len(sanitized_cache.property_assignments), 1)
self.assertEqual(sanitized_cache.get_property_assignment('GenProp0710'), 'YES')
def test_cache_flush(self):
"""Test that the cache can be properly flushed."""
test_cache = AssignmentCache()
test_cache.cache_property_assignment('GenProp0067', 'YES')
test_cache.cache_property_assignment('GenProp0092', 'NO')
test_cache.cache_step_assignment('GenProp0067', 1, 'YES')
test_cache.cache_step_assignment('GenProp0092', 1, 'NO')
test_cache.flush_property_from_cache('GenProp0067')
self.assertEqual(test_cache.get_property_assignment("GenProp0067"),
None)
self.assertEqual(test_cache.get_step_assignment("GenProp0067", 1),
None)
self.assertEqual(len(test_cache.property_assignments), 1)
self.assertEqual(len(test_cache.step_assignments), 1)
def setUpClass(cls):
"""Set up testing data for testing."""
prebuilt_cache = AssignmentCache()
prebuilt_cache.cache_property_assignment('GenProp0053', 'YES')
prebuilt_cache.cache_property_assignment('GenProp0052', 'NO')
prebuilt_cache.cache_property_assignment('GenProp0051', 'PARTIAL')
prebuilt_cache.cache_step_assignment('GenProp0053', 1, 'YES')
prebuilt_cache.cache_step_assignment('GenProp0053', 2, 'NO')
prebuilt_cache.cache_step_assignment('GenProp0053', 3, 'YES')
cls.cache = prebuilt_cache
"""
Test Properties Rooted DAG Structure:
--> GenProp0089
GenProp0066
--> GenProp0092
"""
property_rows_one = [('AC', 'GenProp0066'),
('DE', 'Coenzyme F420 utilization'),
('TP', 'GUILD'), ('--', ''), ('SN', '1'),
('ID', 'Selfish genetic elements'), ('RQ', '0'),
('EV', 'GenProp0089;'), ('--', ''), ('SN', '2'),
('ID', 'Selfish genetic elements'), ('RQ', '0'),
('EV', 'GenProp0092;')]
property_rows_two = [('AC', 'GenProp0089'),
('DE', 'Coenzyme F420 utilization'),
('TP', 'GUILD'), ('--', ''), ('SN', '1'),
('ID', 'LLM-family F420-associated subfamilies'),
('RQ', '0'),
('EV', 'IPR019910; TIGR03564; sufficient;')]
property_rows_three = [('AC', 'GenProp0092'),
('DE', 'Coenzyme F420 utilization'),
('TP', 'GUILD'), ('--', ''), ('SN', '1'),
('ID',
'LLM-family F420-associated subfamilies'),
('RQ', '0'),
('EV', 'IPR019910; TIGR03565; sufficient;')]
property_one = parse_genome_property(property_rows_one)
property_two = parse_genome_property(property_rows_two)
property_three = parse_genome_property(property_rows_three)
raw_properties = [property_one, property_two, property_three]
cls.tree = GenomePropertiesTree(*raw_properties)