def test_options(self):
options = Namespace()
for threshold in [0., 0.5, 1.0]:
options.tta_threshold = threshold
assert not tta.check_options(options)
options.tta_threshold = 1.01
assert tta.check_options(options) == [
"Supplied threshold is out of range 0 to 1: 1.01"
]
options.tta_threshold = -0.01
assert tta.check_options(options) == [
"Supplied threshold is out of range 0 to 1: -0.01"
]
def test_nisin(self):
record = parse_input_sequence(helpers.get_path_to_nisin_with_detection())[0]
clusters = record.get_clusters()
assert clusters
for cluster in clusters:
assert cluster.cds_children
assert record.get_cds_features_within_clusters()
before_count = record.get_feature_count()
assert tta.check_prereqs() == []
assert tta.check_options(self.options) == []
assert tta.is_enabled(self.options)
prior_results = None
results = tta.run_on_record(record, prior_results, self.options)
assert isinstance(results, ModuleResults)
assert len(results.features) == 174
assert record.get_feature_count() == before_count
results.add_to_record(record)
assert record.get_feature_count() == before_count + 174
def test_nisin(self):
record = Record.from_genbank(
helpers.get_path_to_nisin_with_detection(), taxon="bacteria")[0]
regions = record.get_regions()
assert regions
for region in regions:
assert region.cds_children
assert record.get_cds_features_within_regions()
before_count = record.get_feature_count()
assert tta.check_prereqs() == []
assert tta.check_options(self.options) == []
assert tta.is_enabled(self.options)
prior_results = None
results = tta.run_on_record(record, prior_results, self.options)
assert isinstance(results, ModuleResults)
assert len(results.features) == 174
assert record.get_feature_count() == before_count
results.add_to_record(record)
assert record.get_feature_count() == before_count + 174