def test_nisin(self):
"Test lanthipeptide prediction for nisin A"
rec = Record.from_biopython(seqio.read(
helpers.get_path_to_nisin_with_detection()),
taxon="bacteria")
assert not rec.get_cds_motifs()
result = run_specific_analysis(rec)
assert len(result.clusters) == 1
motifs = self.gather_all_motifs(result)
assert len(motifs) == 1
assert not rec.get_cds_motifs()
result.add_to_record(rec)
assert len(rec.get_cds_motifs()) == 1
prepeptide = motifs[0]
# real monoisotopic mass is 3351.51, but we overpredict a Dha
self.assertAlmostEqual(3333.6,
prepeptide.monoisotopic_mass,
delta=0.05)
# real mw is 3354.5, see above
self.assertAlmostEqual(3336.0, prepeptide.molecular_weight, delta=0.05)
for expected, calculated in zip([3354.0, 3372.1, 3390.1, 3408.1],
prepeptide.alternative_weights):
self.assertAlmostEqual(expected, calculated, delta=0.05)
assert prepeptide.lan_bridges == 5
self.assertEqual("MSTKDFNLDLVSVSKKDSGASPR", prepeptide.leader)
self.assertEqual("ITSISLCTPGCKTGALMGCNMKTATCHCSIHVSK", prepeptide.core)
self.assertEqual('Class I', prepeptide.peptide_subclass)
initial_json = result.to_json()
regenerated = LanthiResults.from_json(initial_json, rec)
assert list(result.motifs_by_locus) == ["nisB"]
assert str(result.motifs_by_locus) == str(regenerated.motifs_by_locus)
assert result.clusters == regenerated.clusters
assert initial_json == regenerated.to_json()
def setUp(self):
options = build_config(self.get_args(),
isolated=True,
modules=antismash.get_all_modules())
self.old_config = get_config().__dict__
self.options = update_config(options)
self.record = self.build_record(
helpers.get_path_to_nisin_with_detection())
prepare_data()
def test_result_conversion(self):
nisin = Record.from_genbank(helpers.get_path_to_nisin_with_detection())[0]
with open(path.get_full_path(__file__, "data", "nisin.out")) as handle:
trimmed_output = handle.read()
with patch.object(subprocessing, "run_diamond_search", return_value=trimmed_output):
results = cluster_compare.run_on_record(nisin, None, self.options)
assert results.by_database["MIBiG"].by_region[1]
# ensure JSON conversion of results gives the same result
raw = json.loads(json.dumps(results.to_json()))
regenerated = cluster_compare.regenerate_previous_results(raw, nisin, self.options)
regen_raw = json.loads(json.dumps(regenerated.to_json()))
assert regen_raw == raw
def test_nisin(self):
genbank = helpers.get_path_to_nisin_with_detection()
results = helpers.run_and_regenerate_results_for_module(genbank, rrefinder, self.options)
assert isinstance(results, rrefinder.RREFinderResults)
assert results.bitscore_cutoff == self.options.rre_cutoff
assert results.min_length == self.options.rre_min_length
assert results.record_id == 'HM219853.1'
assert len(results.features) == 1
feature = results.features[0]
assert feature.locus_tag == 'nisB'
assert feature.score == 34.9
assert feature.protein_location == FeatureLocation(141, 228)
assert feature.domain == 'Lanthipeptide_RRE'
assert feature.translation == 'FTRNNANYKFGDRVFQVYTINSSELEEVNIKYTNVYQIISEFC' +
'ENDYQKYEDICETVTLCYGDEYRELSEQYLGSLIVNHYLISNLQK'
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 setUp(self):
self.old_config = get_config().__dict__
options = build_config(self.get_args(),
isolated=True,
modules=antismash.get_all_modules())
self.options = update_config(options)
update_config({"cpus": 1})
# prevent multiprocess testing from taking place, to stop signals
# being caught awkwardly in the test itself
# as smcogs_trees depends on genefunctions.smcogs' data, ensure that's ready to go
assert genefunctions.prepare_data() == []
assert smcog_trees.check_prereqs() == []
assert smcog_trees.check_options(self.options) == []
assert smcog_trees.is_enabled(self.options)
self.record = self.build_record(
helpers.get_path_to_nisin_with_detection())
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
def setUp(self):
options = build_config(self.get_args(),
isolated=True,
modules=antismash.get_all_modules())
self.old_config = get_config().__dict__
self.options = update_config(options)
assert smcogs.check_prereqs() == []
assert smcogs.check_options(self.options) == []
assert smcogs.is_enabled(self.options)
self.record = self.build_record(
helpers.get_path_to_nisin_with_detection())
def serial_run_func(function, arg_sets, _timeout=None):
for arg_set in arg_sets:
function(*arg_set)
self.old_parallel = subprocessing.parallel_function
subprocessing.parallel_function = serial_run_func
