def setUp(self):
self.genes = []
self.clusters = []
domain_names = self.gen_domain_names()
for product in ['not_atpks', 'transatpks']:
cluster = helpers.DummyCluster(1, 2, products=[product])
assert cluster.products == (product, )
for i in range(7):
locus_tag = chr(ord('a') + i)
if i == 6:
locus_tag = "all"
cds = helpers.DummyCDS(1, 2, locus_tag=locus_tag)
cds.product = product
cds.nrps_pks = DummyNRPSQualfier()
cds.nrps_pks.domain_names = domain_names["nrpspksdomains_" +
locus_tag]
cds.cluster = cluster
cluster.add_cds(cds)
self.genes.append(cds)
self.clusters.append(cluster)
self.predictions = [
'redmxmal', 'ccmal', 'ohemal', 'ohmxmal', 'ohmmal', 'ccmmal',
'emal', 'redmmal', 'mmal', 'ccmxmal', 'mxmal', 'redemal', 'ohmal',
'mal', 'ccemal'
]
def test_orphaned_supercluster_number(self):
record = Record("A" * 1000)
cluster = helpers.DummyCluster(0, 1000)
supercluster = SuperCluster(SuperCluster.kinds.SINGLE, [cluster])
with self.assertRaisesRegex(ValueError,
"SuperCluster not contained in record"):
print(record.get_supercluster_number(supercluster))
def test_cluster_numbering(self):
record = Record(Seq("A"*1000))
for start, end in [(50, 100), (10, 40), (700, 1000), (0, 9)]:
cluster = helpers.DummyCluster(start, end)
record.add_cluster(cluster)
for i, cluster in enumerate(sorted(list(record.get_clusters()))):
assert cluster.get_cluster_number() == i + 1
def test_classification_with_colon(self):
# since SMCOG id and description are stored in a string separated by :,
# ensure that descriptions containing : are properly handled
# test gene is AQF52_5530 from CP013129.1
translation = (
"MDTHQREEDPVAARRDRTHYLYLAVIGAVLLGIAVGFLAPGVAVELKPLGTGFVN"
"LIKMMISPIIFCTIVLGVGSVRKAAKVGAVGGLALGYFLVMSTVALAIGLLVGNL"
"LEPGSGLHLTKEIAEAGAKQAEGGGESTPDFLLGIIPTTFVSAFTEGEVLQTLLV"
"ALLAGFALQAMGAAGEPVLRGIGHIQRLVFRILGMIMWVAPVGAFGAIAAVVGAT"
"GAAALKSLAVIMIGFYLTCGLFVFVVLGAVLRLVAGINIWTLLRYLGREFLLILS"
"TSSSESALPRLIAKMEHLGVSKPVVGITVPTGYSFNLDGTAIYLTMASLFVAEAM"
"GDPLSIGEQISLLVFMIIASKGAAGVTGAGLATLAGGLQSHRPELVDGVGLIVGI"
"DRFMSEARALTNFAGNAVATVLVGTWTKEIDKARVTEVLAGNIPFDEKTLVDDHA"
"PVPVPDQRAEGGEEKARAGV")
cds = helpers.DummyCDS(0, len(translation))
cds.translation = translation
results = smcogs.classify("test", [cds], get_config())
assert results.best_hits[cds.get_name(
)].hit_id == "SMCOG1212:sodium:dicarboxylate symporter"
record = helpers.DummyRecord(seq=translation)
record.add_cds_feature(cds)
record.add_cluster(helpers.DummyCluster(0, len(translation)))
# if we don't handle multiple semicolons right, this line will crash
results.add_to_record(record)
gene_functions = cds.gene_functions.get_by_tool("smcogs")
assert len(gene_functions) == 1
assert str(gene_functions[0]).startswith(
"transport (smcogs) SMCOG1212:sodium:dicarboxylate symporter"
" (Score: 416; E-value: 2.3e-126)")
def test_orphaned_cluster_number(self):
record = Record(Seq("A" * 1000))
cluster = helpers.DummyCluster(0, 1000)
with self.assertRaisesRegex(ValueError, "Cluster not contained in record"):
print(record.get_cluster_number(cluster))
with self.assertRaisesRegex(ValueError, "Cluster not contained in record"):
print(cluster.get_cluster_number())
def test_cluster_numbering(self):
features = []
for start, end in self.pairs:
cluster = helpers.DummyCluster(start, end)
self.record.add_cluster(cluster)
features.append(cluster)
features = sorted(features)
for i, cluster in enumerate(self.record.get_clusters()):
assert cluster.get_cluster_number() == i + 1
assert self.record.get_cluster(i + 1) is features[i]
def test_cds_cluster_linkage(self):
record = Record("A"*200)
for start, end in [(50, 100), (10, 90), (0, 9), (150, 200)]:
record.add_cds_feature(helpers.DummyCDS(start, end))
for start, end in [(10, 120), (5, 110), (10, 160), (45, 200)]:
record.clear_clusters()
cluster = helpers.DummyCluster(start, end)
record.add_cluster(cluster)
assert len(cluster.cds_children) == 2
for cds in cluster.cds_children:
assert cds.overlaps_with(cluster)
def test_supercluster_numbering(self):
features = []
for location in self.locations:
supercluster = SuperCluster(
SuperCluster.kinds.SINGLE,
[helpers.DummyCluster(location.start, location.end)])
self.record.add_supercluster(supercluster)
features.append(supercluster)
features = sorted(features)
for i, cluster in enumerate(self.record.get_superclusters()):
assert cluster.get_supercluster_number() == i + 1
assert self.record.get_supercluster(i + 1) is features[i]
def test_classification_with_colon(self):
# since SMCOG id and description are stored in a string separated by :,
# ensure that descriptions containing : are properly handled
cds = helpers.DummyCDS(locus_tag="test")
record = helpers.DummyRecord(features=[cds], seq="A" * 100)
record.add_cluster(helpers.DummyCluster(0, 100))
results = SMCOGResults(record.id)
results.best_hits[cds.get_name()] = HMMResult(
"SMCOG1212:sodium:dicarboxylate_symporter", 0, 100, 2.3e-126, 416)
results.add_to_record(record)
gene_functions = cds.gene_functions.get_by_tool("smcogs")
assert len(gene_functions) == 1
assert str(gene_functions[0]).startswith(
"transport (smcogs) SMCOG1212:sodium:dicarboxylate_symporter"
" (Score: 416; E-value: 2.3e-126)")
def test_cds_removal(self):
record = Record(Seq("A" * 1000))
cluster = helpers.DummyCluster(0, 1000)
record.add_cluster(cluster)
first_cds = helpers.DummyCDS(0, 100, locus_tag="A")
second_cds = helpers.DummyCDS(200, 300, locus_tag="B")
record.add_cds_feature(first_cds)
record.add_cds_feature(second_cds)
assert len(record.get_cds_features()) == 2
assert len(cluster.cds_children) == 2
record.remove_cds_feature(first_cds)
assert len(record.get_cds_features()) == 1
assert len(cluster.cds_children) == 1
assert record.get_cds_features()[0] is list(cluster.cds_children)[0]
assert record.get_cds_features()[0].locus_tag == "B"