def strip_record(record: Record) -> None:
""" Discard antismash specific features and feature qualifiers """
logging.debug(
"Stripping antiSMASH features and annotations from record: %s",
record.id)
record.clear_clusters()
record.clear_cluster_borders()
record.clear_cds_motifs()
record.clear_antismash_domains()
record.clear_pfam_domains()
# clean up antiSMASH annotations in CDS features
for feature in record.get_cds_features():
feature.sec_met = None
feature.gene_functions.clear()
def strip_record(record: Record) -> None:
""" Discard antismash specific features and feature qualifiers """
logging.debug(
"Stripping antiSMASH features and annotations from record: %s",
record.id)
record.clear_clusters()
record.clear_superclusters()
record.clear_subregions()
record.clear_regions()
record.clear_antismash_domains()
record.clear_pfam_domains()
# clean up antiSMASH-created CDSMotifs, but leave the rest
motifs = list(record.get_cds_motifs())
record.clear_cds_motifs()
for motif in motifs:
if not motif.created_by_antismash:
record.add_cds_motif(motif)
# clean up antiSMASH annotations in CDS features
for feature in record.get_cds_features():
feature.sec_met = SecMetQualifier()
feature.gene_functions.clear()
class TestSuperCluster(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_cluster(cluster)
def test_kinds_attachment(self):
assert SuperCluster.kinds == SuperClusterKind
def test_record_linkage(self):
cluster = SuperCluster(SuperCluster.kinds.INTERLEAVED,
self.record.get_clusters())
with self.assertRaisesRegex(ValueError,
"SuperCluster not contained in record"):
cluster.get_supercluster_number()
self.record.add_supercluster(cluster)
assert cluster.get_supercluster_number() == 1
def test_bad_kind(self):
with self.assertRaisesRegex(TypeError, "should be SuperClusterKind"):
SuperCluster("berf", self.record.get_clusters())
def test_no_clusters(self):
with self.assertRaisesRegex(ValueError,
"cannot exist without at least one"):
SuperCluster(SuperCluster.kinds.INTERLEAVED, [])
def test_rules(self):
cluster = SuperCluster(SuperCluster.kinds.INTERLEAVED,
self.record.get_clusters())
assert cluster.detection_rules == [
cluster.detection_rule for cluster in self.record.get_clusters()
]
def test_smiles_and_polymer(self):
cluster = SuperCluster(SuperCluster.kinds.INTERLEAVED,
self.record.get_clusters())
assert cluster.smiles_structure is None
assert cluster.polymer is None
def test_conversion(self):
kind = SuperClusterKind.INTERLEAVED
original = SuperCluster(kind,
self.record.get_clusters(),
smiles="dummy smiles",
polymer="dummy polymer")
self.record.add_supercluster(original)
assert original.products == ["a"]
assert len(original.clusters) == 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_supercluster_number())
]
assert bio.qualifiers["SMILES"] == ["dummy smiles"]
assert bio.qualifiers["polymer"] == ["dummy polymer"]
assert bio.qualifiers["contig_edge"] == ["True"]
regenerated = SuperCluster.from_biopython(bio)
assert isinstance(regenerated, TemporarySuperCluster)
assert regenerated.products == original.products
assert regenerated.location == original.location
assert regenerated.smiles_structure == original.smiles_structure
assert regenerated.polymer == original.polymer
assert regenerated.clusters == [
cluster.get_cluster_number()
for cluster in self.record.get_clusters()
]
assert regenerated.kind == original.kind
real = regenerated.convert_to_real_feature(self.record)
assert isinstance(real, SuperCluster)
assert len(real.clusters) == len(self.record.get_clusters())
for reference, record_cluster in zip(real.clusters,
self.record.get_clusters()):
assert reference is record_cluster
# attempt a conversion with a record missing the cluster
self.record.clear_clusters()
with self.assertRaisesRegex(ValueError,
"Not all referenced clusters are present"):
regenerated.convert_to_real_feature(self.record)
