def test_jc(self):
jc = spectraltree.Jukes_Cantor()
observations, meta = spectraltree.simulate_sequences(
seq_len=500,
tree_model=self.reference_tree,
seq_model=jc,
mutation_rate=0.05,
rng=np.random.default_rng(12345),
alphabet='DNA')
spectral_method = spectraltree.STDR(spectraltree.RAxML,
spectraltree.JC_similarity_matrix)
#spectral_method = spectraltree.STDR(spectraltree.NeighborJoining,spectraltree.JC_similarity_matrix)
tree_rec = spectral_method.deep_spectral_tree_reconstruction(
observations,
spectraltree.JC_similarity_matrix,
taxa_metadata=meta,
threshhold=self.threshold,
min_split=5,
merge_method="least_square",
verbose=False)
self.assertTrue(spectraltree.topos_equal(self.reference_tree,
tree_rec))
def test_hky_similarity(self):
observationsHKY, metaHKY = spectraltree.simulate_sequences(
seq_len=2_000,
tree_model=self.reference_tree,
seq_model=spectraltree.HKY(kappa=1.5),
mutation_rate=0.1,
rng=default_rng(543),
alphabet="DNA")
nj_hky = spectraltree.NeighborJoining(spectraltree.HKY_similarity_matrix(metaHKY))
self.assertTrue(spectraltree.topos_equal(self.reference_tree, nj_hky(observationsHKY, metaHKY)))
def test_jukes_cantor_similarity(self):
observationsJC, metaJC = spectraltree.simulate_sequences(
seq_len=400,
tree_model=self.reference_tree,
seq_model=spectraltree.Jukes_Cantor(),
mutation_rate=0.1,
rng=default_rng(345),
alphabet="DNA")
nj_jc = spectraltree.NeighborJoining(spectraltree.JC_similarity_matrix)
self.assertTrue(spectraltree.topos_equal(self.reference_tree, nj_jc(observationsJC, metaJC)))
def test_hky(self):
spectral_method = spectraltree.STR(spectraltree.RAxML,
spectraltree.HKY_similarity_matrix(
self.meta_hky),
threshold=32,
merge_method="least_square",
num_gaps=1,
min_split=5,
verbose=False)
self.assertTrue(
spectraltree.topos_equal(
self.reference_tree,
spectral_method(self.observations_hky, self.meta_hky)))
def test_hky(self):
observationsHKY, metaHKY = spectraltree.simulate_sequences(
seq_len=500,
tree_model=self.reference_tree,
seq_model=spectraltree.HKY(kappa=2),
mutation_rate=0.1,
rng=default_rng(234),
alphabet="DNA")
forrest = spectraltree.Forrest()
self.assertTrue(
spectraltree.topos_equal(self.reference_tree,
forrest(observationsHKY, metaHKY)))
def test_jukes_cantor(self):
observationsJC, metaJC = spectraltree.simulate_sequences(
seq_len=500,
tree_model=self.reference_tree,
seq_model=spectraltree.Jukes_Cantor(),
mutation_rate=0.1,
rng=default_rng(234),
alphabet="DNA")
forrest = spectraltree.Forrest()
self.assertTrue(
spectraltree.topos_equal(self.reference_tree,
forrest(observationsJC, metaJC)))
def test_jukes_cantor(self):
# reference_tree = spectraltree.unrooted_birth_death_tree(num_taxa, birth_rate=1, rng=)
# reference_tree = spectraltree.lopsided_tree(num_taxa)
reference_tree = spectraltree.balanced_binary(8)
jc = spectraltree.Jukes_Cantor(num_classes=2)
observations, meta = spectraltree.simulate_sequences(
seq_len=10_000,
tree_model=reference_tree,
seq_model=jc,
mutation_rate=jc.p2t(0.98),
rng=default_rng(678),
alphabet="Binary")
rg = spectraltree.RG(spectraltree.JC_distance_matrix)
recoverd_tree = rg(observations, meta)
print("(RF distance,F1 score):",
spectraltree.compare_trees(reference_tree, recoverd_tree))
self.assertTrue(spectraltree.topos_equal(
reference_tree, recoverd_tree)) # this doesn't work very well