def test_probabilities(self):
loc = FeatureLocation(0, 10)
candidates = [DummyCandidateCluster([create_protocluster(0, 10)])]
assert Region(candidate_clusters=candidates).probabilities == []
subs = [SubRegion(loc, "testtool", probability=None)]
assert Region(candidate_clusters=candidates, subregions=subs).probabilities == []
subs.append(SubRegion(loc, "testtool", probability=0.1))
assert Region(candidate_clusters=candidates, subregions=subs).probabilities == [0.1]
subs.append(SubRegion(loc, "testtool", probability=0.7))
assert Region(candidate_clusters=candidates, subregions=subs).probabilities == [0.1, 0.7]
def test_probabilities(self):
loc = FeatureLocation(0, 10)
supers = [
SuperCluster(SuperCluster.kinds.SINGLE, [create_cluster(0, 10)])
]
assert Region(superclusters=supers).probabilities == []
subs = [SubRegion(loc, "testtool", probability=None)]
assert Region(superclusters=supers,
subregions=subs).probabilities == []
subs.append(SubRegion(loc, "testtool", probability=0.1))
assert Region(superclusters=supers,
subregions=subs).probabilities == [0.1]
subs.append(SubRegion(loc, "testtool", probability=0.7))
assert Region(superclusters=supers,
subregions=subs).probabilities == [0.1, 0.7]
def test_genbank(self):
dummy_record = Record(Seq("A" * 100, generic_dna))
clusters = [
create_cluster(3, 20, "prodA"),
create_cluster(25, 41, "prodB")
]
for cluster in clusters:
dummy_record.add_cluster(cluster)
subregion = SubRegion(FeatureLocation(35, 71), "test", 0.7)
dummy_record.add_subregion(subregion)
supercluster = SuperCluster(SuperCluster.kinds.NEIGHBOURING, clusters)
dummy_record.add_supercluster(supercluster)
region = Region(superclusters=[supercluster], subregions=[subregion])
dummy_record.add_region(region)
with NamedTemporaryFile(suffix=".gbk") as output:
region.write_to_genbank(output.name)
bio = list(seqio.parse(output.name))
assert len(bio) == 1
rec = Record.from_biopython(bio[0], taxon="bacteria")
assert len(rec.get_regions()) == 1
new = rec.get_region(0)
assert new.location.start == 3 - region.location.start
assert new.location.end == 71 - region.location.start
assert new.products == region.products
assert new.probabilities == region.probabilities
def test_limited_add_cds_propagation(self):
cds = DummyCDS(0, 10)
self.sub = SubRegion(FeatureLocation(20, 30), "testtool")
self.region = Region(superclusters=[self.super], subregions=[self.sub])
# ensure all empty to start with
assert not self.cluster.cds_children
assert not self.super.cds_children
assert not self.sub.cds_children
assert not self.region.cds_children
assert not cds.region
self.region.add_cds(cds)
assert self.cluster.cds_children == (cds, )
assert self.super.cds_children == (cds, )
assert not self.sub.cds_children
assert self.region.cds_children == (cds, )
assert cds.region is self.region
def test_sideloaded(self):
clusters = [
create_protocluster(3, 20, "prodA"),
SideloadedProtocluster(FeatureLocation(25, 41),
FeatureLocation(25, 41), "external",
"prodB")
]
candidate = CandidateCluster(CandidateCluster.kinds.NEIGHBOURING,
clusters)
subregions = [
SubRegion(FeatureLocation(35, 71), "test", 0.7),
SideloadedSubRegion(FeatureLocation(45, 61), "external")
]
region = Region(candidate_clusters=[candidate], subregions=subregions)
sideloaded = region.get_sideloaded_areas()
assert len(sideloaded) == 2
assert sideloaded[0] is clusters[1]
assert sideloaded[1] is subregions[1]
def test_orphaned(self):
sub = SubRegion(FeatureLocation(0, 10), tool="test")
assert not sub.parent_record
with self.assertRaisesRegex(ValueError, "not in a record"):
sub.get_subregion_number()
def test_anchor(self):
loc = FeatureLocation(0, 10)
assert SubRegion(loc, tool="test").anchor == ""
assert SubRegion(loc, tool="test", anchor="anch").anchor == "anch"
def test_probability(self):
loc = FeatureLocation(0, 10)
assert SubRegion(loc, tool="test").probability is None
assert SubRegion(loc, tool="test", probability=9.5).probability == 9.5
assert SubRegion(loc, tool="test", probability=.5).probability == .5
def setUp(self):
self.cluster = create_cluster(0, 10)
self.super = SuperCluster(SuperCluster.kinds.SINGLE, [self.cluster])
self.sub = SubRegion(self.cluster.location, "testtool")
self.region = Region(superclusters=[self.super], subregions=[self.sub])
def setUp(self):
self.protocluster = DummyProtocluster()
self.candidate = DummyCandidateCluster([self.protocluster])
self.sub = SubRegion(self.protocluster.location, "testtool")
self.region = Region(candidate_clusters=[self.candidate],
subregions=[self.sub])
