class TestCandidateCluster(unittest.TestCase):
def setUp(self):
self.record = Record(Seq("A" * 100))
clusters = [create_cluster(0, 0, 10, 10)]
for cluster in clusters:
self.record.add_protocluster(cluster)
def test_kinds_attachment(self):
assert CandidateCluster.kinds == CandidateClusterKind
def test_record_linkage(self):
cluster = CandidateCluster(CandidateCluster.kinds.INTERLEAVED,
self.record.get_protoclusters())
with self.assertRaisesRegex(
ValueError, "CandidateCluster not contained in record"):
cluster.get_candidate_cluster_number()
self.record.add_candidate_cluster(cluster)
assert cluster.get_candidate_cluster_number() == 1
def test_bad_kind(self):
with self.assertRaisesRegex(TypeError,
"should be CandidateClusterKind"):
CandidateCluster("berf", self.record.get_protoclusters())
def test_no_clusters(self):
with self.assertRaisesRegex(ValueError,
"cannot exist without at least one"):
CandidateCluster(CandidateCluster.kinds.INTERLEAVED, [])
def test_rules(self):
cluster = CandidateCluster(CandidateCluster.kinds.INTERLEAVED,
self.record.get_protoclusters())
assert cluster.detection_rules == [
cluster.detection_rule
for cluster in self.record.get_protoclusters()
]
def test_smiles_and_polymer(self):
cluster = CandidateCluster(CandidateCluster.kinds.INTERLEAVED,
self.record.get_protoclusters())
assert cluster.smiles_structure is None
assert cluster.polymer is None
def test_conversion(self):
kind = CandidateClusterKind.INTERLEAVED
original = CandidateCluster(kind,
self.record.get_protoclusters(),
smiles="dummy smiles",
polymer="dummy polymer")
self.record.add_candidate_cluster(original)
assert original.products == ["a"]
assert len(original.protoclusters) == 1
bios = original.to_biopython()
assert len(bios) == 1
bio = bios[0]
assert bio.qualifiers["product"] == ["a"]
assert bio.qualifiers["kind"] == [str(kind)]
assert bio.qualifiers["candidate_cluster_number"] == [
str(original.get_candidate_cluster_number())
]
assert bio.qualifiers["SMILES"] == ["dummy smiles"]
assert bio.qualifiers["polymer"] == ["dummy polymer"]
assert bio.qualifiers["contig_edge"] == ["True"]
real = CandidateCluster.from_biopython(bio, record=self.record)
assert isinstance(real, CandidateCluster)
assert len(real.protoclusters) == len(self.record.get_protoclusters())
for reference, record_cluster in zip(real.protoclusters,
self.record.get_protoclusters()):
assert reference is record_cluster
# attempt a conversion with a record missing the cluster
self.record.clear_protoclusters()
with self.assertRaisesRegex(
ValueError,
"record does not contain all expected protoclusters"):
CandidateCluster.from_biopython(bio, record=self.record)
# and with no record
with self.assertRaisesRegex(ValueError, "record instance required"):
CandidateCluster.from_biopython(bio)
def test_core(self):
protos = [
create_cluster(5, 10, 20, 25, "a"),
create_cluster(30, 40, 50, 60, "b")
]
cluster = CandidateCluster(CandidateClusterKind.NEIGHBOURING,
protos,
smiles="dummy",
polymer="dummy")
assert cluster.core_location == FeatureLocation(10, 50)
def test_comparison(self):
candidate = CandidateCluster(CandidateClusterKind.NEIGHBOURING,
[create_cluster(5, 10, 20, 25, "a")])
longer = CandidateCluster(CandidateClusterKind.NEIGHBOURING,
[create_cluster(5, 10, 40, 45, "a")])
after = CandidateCluster(CandidateClusterKind.NEIGHBOURING,
[create_cluster(10, 20, 40, 45, "a")])
def check(first, second):
assert first < second
assert first < second.location
assert sorted([second, first]) == [first, second]
check(candidate, after)
check(longer, candidate)
check(longer, after)
assert sorted([after, candidate, longer]) == [longer, candidate, after]
class TestCandidateCluster(unittest.TestCase):
def setUp(self):
self.record = Record(Seq("A" * 100))
clusters = [create_cluster(0, 0, 10, 10)]
for cluster in clusters:
self.record.add_protocluster(cluster)
def test_kinds_attachment(self):
assert CandidateCluster.kinds == CandidateClusterKind
def test_record_linkage(self):
cluster = CandidateCluster(CandidateCluster.kinds.INTERLEAVED,
self.record.get_protoclusters())
with self.assertRaisesRegex(
ValueError, "CandidateCluster not contained in record"):
cluster.get_candidate_cluster_number()
self.record.add_candidate_cluster(cluster)
assert cluster.get_candidate_cluster_number() == 1
def test_bad_kind(self):
with self.assertRaisesRegex(TypeError,
"should be CandidateClusterKind"):
CandidateCluster("berf", self.record.get_protoclusters())
def test_no_clusters(self):
with self.assertRaisesRegex(ValueError,
"cannot exist without at least one"):
CandidateCluster(CandidateCluster.kinds.INTERLEAVED, [])
def test_rules(self):
cluster = CandidateCluster(CandidateCluster.kinds.INTERLEAVED,
self.record.get_protoclusters())
assert cluster.detection_rules == [
cluster.detection_rule
for cluster in self.record.get_protoclusters()
]
def test_smiles_and_polymer(self):
cluster = CandidateCluster(CandidateCluster.kinds.INTERLEAVED,
self.record.get_protoclusters())
assert cluster.smiles_structure is None
assert cluster.polymer is None
def test_conversion(self):
kind = CandidateClusterKind.INTERLEAVED
original = CandidateCluster(kind,
self.record.get_protoclusters(),
smiles="dummy smiles",
polymer="dummy polymer")
self.record.add_candidate_cluster(original)
assert original.products == ["a"]
assert len(original.protoclusters) == 1
bios = original.to_biopython()
assert len(bios) == 1
bio = bios[0]
assert bio.qualifiers["product"] == ["a"]
assert bio.qualifiers["kind"] == [str(kind)]
assert bio.qualifiers["candidate_cluster_number"] == [
str(original.get_candidate_cluster_number())
]
assert bio.qualifiers["SMILES"] == ["dummy smiles"]
assert bio.qualifiers["polymer"] == ["dummy polymer"]
assert bio.qualifiers["contig_edge"] == ["True"]
regenerated = CandidateCluster.from_biopython(bio)
assert isinstance(regenerated, TemporaryCandidateCluster)
assert regenerated.products == original.products
assert regenerated.location == original.location
assert regenerated.smiles_structure == original.smiles_structure
assert regenerated.polymer == original.polymer
proto_numbers = [
cluster.get_protocluster_number()
for cluster in self.record.get_protoclusters()
]
assert regenerated.protoclusters == proto_numbers
assert regenerated.kind == original.kind
real = regenerated.convert_to_real_feature(self.record)
assert isinstance(real, CandidateCluster)
assert len(real.protoclusters) == len(self.record.get_protoclusters())
for reference, record_cluster in zip(real.protoclusters,
self.record.get_protoclusters()):
assert reference is record_cluster
# attempt a conversion with a record missing the cluster
self.record.clear_protoclusters()
with self.assertRaisesRegex(ValueError,
"Not all referenced clusters are present"):
regenerated.convert_to_real_feature(self.record)