def test_hybrid_interactions(self):
cluster = create_cluster(3, 8, 171, 176, "a")
hybrid = create_cluster(3, 8, 50, 55, "b")
contained = create_cluster(80, 90, 100, 110,
"c") # will form part of hybrid
hybrid_cds = create_cds(8, 50, ["a", "b"])
cluster.add_cds(hybrid_cds)
hybrid.add_cds(hybrid_cds)
for overlapping in [
create_cluster(120, 130, 200, 250, "d"),
create_cluster(60, 70, 200, 250, "d")
]:
created = creator([cluster, hybrid, contained, overlapping])
assert len(created) == 2
assert created[0].location == FeatureLocation(3, 250)
assert created[0].kind == CandidateCluster.kinds.INTERLEAVED
assert created[0].protoclusters == tuple(
sorted([cluster, hybrid, contained, overlapping]))
assert created[1].location == FeatureLocation(3, 176)
assert created[1].kind == CandidateCluster.kinds.CHEMICAL_HYBRID
assert created[1].protoclusters == (cluster, hybrid, contained)
def test_contained_neighbours(self):
big = create_cluster(0, 100, 130, 230, "a")
small = create_cluster(10, 20, 30, 40, "b")
created = creator([big, small])
assert len(created) == 2
assert created[0].kind == CandidateCluster.kinds.NEIGHBOURING
assert created[0].location == big.location
assert created[1].kind == CandidateCluster.kinds.SINGLE
assert created[1].location == small.location
def test_creation_coreoverlap(self):
cluster = create_cluster(3, 8, 71, 76, 'a')
extra_cluster = create_cluster(50, 60, 120, 170, 'b')
# create a CDS within both clusters that has a product from only one cluster
cds = create_cds(60, 65, ["a"])
cluster.add_cds(cds)
extra_cluster.add_cds(cds)
created = creator([cluster, extra_cluster])
print(created)
assert len(created) == 1
candidate_cluster = created[0]
assert candidate_cluster.kind == CandidateCluster.kinds.INTERLEAVED
assert candidate_cluster.location == FeatureLocation(3, 170)
def test_interleaving(self):
# these first two hybrid clumps should be interleaved
first_hybrid_clusters = [
create_cluster(30, 60, 120, 150, "a"),
create_cluster(60, 90, 150, 180, "b")
]
cds = create_cds(90, 120, ["a", "b"])
for cluster in first_hybrid_clusters:
cluster.add_cds(cds)
second_hybrid_clusters = [
create_cluster(90, 120, 250, 280, "c"),
create_cluster(190, 220, 280, 310, "d")
]
cds = create_cds(220, 250, ["c", "d"])
for cluster in second_hybrid_clusters:
cluster.add_cds(cds)
# this non-hybrid should also be included in the interleaved
single = create_cluster(230, 250, 410, 430, "e")
# this hybrid should not
standalone = [
create_cluster(1000, 1100, 1400, 1500, "f"),
create_cluster(1100, 1200, 1500, 1600, "g")
]
cds = create_cds(1300, 1400, ["f", "g"])
for cluster in standalone:
cluster.add_cds(cds)
created = creator(first_hybrid_clusters + second_hybrid_clusters +
[single] + standalone)
assert len(created) == 4
assert created[0].location == FeatureLocation(30, 430)
assert created[0].core_location == FeatureLocation(60, 410)
assert created[0].kind == CandidateCluster.kinds.INTERLEAVED
assert created[0].protoclusters == tuple(first_hybrid_clusters +
second_hybrid_clusters +
[single])
assert created[1].location == FeatureLocation(30, 180)
assert created[1].protoclusters == tuple(first_hybrid_clusters)
assert created[2].location == FeatureLocation(90, 310)
assert created[2].protoclusters == tuple(second_hybrid_clusters)
for cand in created[1:3]:
assert cand.kind == CandidateCluster.kinds.CHEMICAL_HYBRID
assert created[3].location == FeatureLocation(1000, 1600)
assert created[3].kind == CandidateCluster.kinds.CHEMICAL_HYBRID
def test_creation_hybrid(self):
cluster = create_cluster(3, 8, 71, 76, 'a')
hybrid_cluster = create_cluster(50, 60, 120, 170, 'b')
# insert the cds that will cause the hybrid call
cds_ab = create_cds(60, 65, ["a", "b"])
cluster.add_cds(cds_ab)
hybrid_cluster.add_cds(cds_ab)
created = creator([cluster, hybrid_cluster])
print(created)
assert len(created) == 1
candidate_cluster = created[0]
assert candidate_cluster.kind == CandidateCluster.kinds.CHEMICAL_HYBRID
assert candidate_cluster.location == FeatureLocation(3, 170)
def test_creation_neighbours(self):
cluster = create_cluster(3, 8, 71, 76, 'a')
extra_cluster = create_cluster(50, 100, 120, 170, 'b')
created = creator([cluster, extra_cluster])
print(created)
assert len(created) == 3
expected_location = FeatureLocation(cluster.location.start,
extra_cluster.location.end)
assert created[
0].kind == CandidateCluster.kinds.NEIGHBOURING and created[
0].location == expected_location
assert created[1].kind == CandidateCluster.kinds.SINGLE and created[
1].location == cluster.location
assert created[2].kind == CandidateCluster.kinds.SINGLE and created[
2].location == extra_cluster.location
def test_interleaving_order(self):
clusters = [
create_cluster(1000, 1100, 1400, 1500, "a"),
create_cluster(1050, 2000, 3000, 4000,
"b"), # sorts second due to neighbouring
create_cluster(1100, 1200, 1500, 1600, "c")
]
assert sorted(clusters) == clusters
created = creator(clusters)
assert len(created) == 3
assert created[0].kind == CandidateCluster.kinds.NEIGHBOURING
assert created[0].location == FeatureLocation(1000, 4000)
assert created[1].kind == CandidateCluster.kinds.INTERLEAVED
assert created[1].location == FeatureLocation(1000, 1600)
assert created[2].kind == CandidateCluster.kinds.SINGLE
assert created[2].location == FeatureLocation(1050, 4000)
def test_multiple_contained_in_hybrid(self):
clusters = [
create_cluster(142916, 162916, 191227, 209850,
"a"), # covers whole region
create_cluster(142916, 162916, 169708, 189708,
"b"), # causes chem hybrid
create_cluster(154261, 174261, 175881, 195881, "c"), # interleaved
create_cluster(160464, 180464, 183155, 203155, "d"), # interleaved
]
cds = create_cds(162916, 169708, ["a", "b"])
clusters[0].add_cds(cds)
clusters[1].add_cds(cds)
created = creator(clusters)
assert len(created) == 1
assert created[0].kind == CandidateCluster.kinds.CHEMICAL_HYBRID
assert created[0].protoclusters == tuple(clusters)
def test_creation_mixed(self):
cluster = create_cluster(3, 8, 71, 76, 'a')
hybrid_cluster = create_cluster(50, 60, 120, 170, 'b')
overlap_cluster = create_cluster(80, 90, 130, 180, 'o')
neighbour_cluster = create_cluster(50, 210, 260, 270, 'a')
isolated_cluster = create_cluster(450, 500, 550, 600, 'alone')
# insert the cds that will cause the hybrid call
cds_ab = create_cds(60, 65, ["a", "b"])
cluster.add_cds(cds_ab)
hybrid_cluster.add_cds(cds_ab)
created = creator([
cluster, hybrid_cluster, overlap_cluster, neighbour_cluster,
isolated_cluster
])
print(created)
assert len(created) == 5
assert created[0].location == FeatureLocation(3, 270)
assert created[0].kind == CandidateCluster.kinds.NEIGHBOURING
assert created[0].protoclusters == (cluster, neighbour_cluster,
hybrid_cluster, overlap_cluster)
assert created[1].location == FeatureLocation(3, 180)
assert created[1].kind == CandidateCluster.kinds.INTERLEAVED
assert created[1].protoclusters == (cluster, hybrid_cluster,
overlap_cluster)
assert created[2].location == FeatureLocation(3, 170)
assert created[2].kind == CandidateCluster.kinds.CHEMICAL_HYBRID
assert created[2].protoclusters == (cluster, hybrid_cluster)
assert created[3].location == FeatureLocation(50, 270)
assert created[3].kind == CandidateCluster.kinds.SINGLE
assert created[3].protoclusters == (neighbour_cluster, )
assert created[4].location == FeatureLocation(450, 600)
assert created[4].kind == CandidateCluster.kinds.SINGLE
assert created[4].protoclusters == (isolated_cluster, )
def test_creation_single(self):
created = creator([create_cluster(3, 8, 71, 76, 'a')])
print(created)
assert len(created) == 1
assert created[0].location == FeatureLocation(3, 76)
assert created[0].kind == CandidateCluster.kinds.SINGLE
def test_creation_empty(self):
assert creator([]) == []
