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_threshold_partition(self):
jc = spectraltree.Jukes_Cantor()
observations, taxa_meta = spectraltree.simulate_sequences(
seq_len=1000,
tree_model=self.reference_tree,
seq_model=jc,
mutation_rate=jc.p2t(0.95),
rng=np.random.default_rng(321))
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=taxa_meta,
num_gaps=4,
threshhold=35)
RF, _ = spectraltree.compare_trees(tree_rec, self.reference_tree)
self.assertEqual(RF, 0)
tree_rec_b = spectral_method.deep_spectral_tree_reconstruction(
observations,
spectraltree.JC_similarity_matrix,
taxa_metadata=taxa_meta,
num_gaps=1,
threshhold=35)
RF_b, _ = spectraltree.compare_trees(tree_rec_b, self.reference_tree)
self.assertEqual(RF_b, 0)
def generate_sequences_gamma(tree, num_taxa, jc, gamma_vec, basic_rate):
observations = np.zeros((num_taxa, len(gamma_vec)))
obs, meta_data = spectraltree.simulate_sequences(1,
tree_model=tree,
seq_model=jc,
mutation_rate=basic_rate *
gamma_vec[0],
alphabet="DNA")
observations[:, 0] = obs[0].T
for idx, gamma in enumerate(gamma_vec[1:]):
obs, meta_data = spectraltree.simulate_sequences(
1,
tree_model=tree,
seq_model=jc,
mutation_rate=basic_rate * gamma,
alphabet="DNA")
observations[:, idx + 1] = obs[0].T
return observations, meta_data
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 setUp(self):
# self.reference_tree = spectraltree.unrooted_birth_death_tree(self.num_taxa, birth_rate=1)
# self.reference_tree = spectraltree.lopsided_tree(self.num_taxa)
self.reference_tree = spectraltree.balanced_binary(128)
# self.reference_tree = spectraltree.unrooted_pure_kingman_tree(self.num_taxa)
self.observations_hky, self.meta_hky = spectraltree.simulate_sequences(
seq_len=300,
tree_model=self.reference_tree,
seq_model=spectraltree.HKY(kappa=2),
mutation_rate=0.05,
rng=np.random.default_rng(234),
alphabet='DNA')
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
def test_angle_least_square(self):
# copied from test_deep_spectral_tree_reonstruction
N = 1000
jc = spectraltree.Jukes_Cantor()
mutation_rate = jc.p2t(0.95)
num_itr = 2 #0
#reference_tree = spectraltree.balanced_binary(num_taxa)
lopsided_reference_tree = spectraltree.lopsided_tree(128)
# reference_tree = spectraltree.unrooted_birth_death_tree(num_taxa, birth_rate=1)
# for x in reference_tree.preorder_edge_iter():
# x.length = 1
merging_method_list = ['least_square', 'angle']
RF = {'least_square': [], 'angle': []}
F1 = {'least_square': [], 'angle': []}
for merge_method in merging_method_list:
for i in range(num_itr):
observations, taxa_meta = spectraltree.simulate_sequences(
seq_len=N,
tree_model=lopsided_reference_tree,
seq_model=jc,
mutation_rate=mutation_rate,
rng=np.random.default_rng(789))
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=taxa_meta,
threshhold=16,
merge_method=merge_method)
RF_i, F1_i = spectraltree.compare_trees(
tree_rec, lopsided_reference_tree)
RF[merge_method].append(RF_i)
F1[merge_method].append(F1_i)
self.assertEqual(np.mean(RF['angle']), 0)
self.assertEqual(np.mean(RF['least_square']), 0)
np.random.seed(0)
reference_tree = spectraltree.unrooted_birth_death_tree(num_taxa, birth_rate=1)
#reference_tree = spectraltree.lopsided_tree(num_taxa)
#reference_tree = spectraltree.balanced_binary(num_taxa)
for x in reference_tree.preorder_edge_iter():
x.length = 1
np.random.seed(0)
cherry_count = cherry_count_for_tree(reference_tree)
print("Orig Cherry count:", cherry_count)
############################################
observations, meta = spectraltree.simulate_sequences(
N,
tree_model=reference_tree,
seq_model=jc,
mutation_rate=mutation_rate,
rng=np.random,
alphabet='DNA')
spectral_method = spectraltree.SpectralTreeReconstruction(
spectraltree.NeighborJoining, spectraltree.JC_similarity_matrix)
tree_rec = spectral_method.deep_spectral_tree_reconstruction(
observations,
spectraltree.JC_similarity_matrix,
taxa_metadata=meta,
threshhold=8,
min_split=3,
merge_method="least_square",
verbose=False)
str_cherry_count = cherry_count_for_tree(tree_rec)
delta_vec = [0.88, 0.9, 0.92, 0.94]
N_vec = [100, 200, 300, 400]
snj = spectraltree.SpectralNeighborJoining(spectraltree.JC_similarity_matrix)
nj = spectraltree.NeighborJoining(spectraltree.JC_similarity_matrix)
print(d.shape)
for i in range(num_itr):
print(i)
A, reference_tree = generate_random_tree_diameter(m)
G = igraph.Graph.Adjacency((A > 0).tolist())
d = G.diameter(directed=False)
for delta in delta_vec:
mutation_rate = jc.p2t(delta)
observations, taxa_meta = spectraltree.simulate_sequences(
max(N_vec),
tree_model=reference_tree,
seq_model=jc,
mutation_rate=mutation_rate,
alphabet="DNA")
for N in N_vec:
# SNJ
t_s = time.time()
tree_snj = snj(observations[:, :N], taxa_meta)
runtime_snj = time.time() - t_s
RF_snj, F1 = spectraltree.compare_trees(tree_snj, reference_tree)
df = df.append(
{
'method': 'SNJ',
'runtime': runtime_snj,
'RF': RF_snj,
'm': m,
print("Creating tree")
jc = spectraltree.Jukes_Cantor()
hky = spectraltree.HKY(kappa=2)
mutation_rate = [jc.p2t(0.95)]
# mutation_rate = [0.1]
#reference_tree = spectraltree.unrooted_birth_death_tree(num_taxa, birth_rate=0.5)
reference_tree = spectraltree.lopsided_tree(num_taxa)
# reference_tree = spectraltree.balanced_binary(num_taxa)
# for x in reference_tree.preorder_edge_iter():
# x.length = 0.5
print("Genration observations by JC and HKY")
observationsJC, metaJC = spectraltree.simulate_sequences(
N,
tree_model=reference_tree,
seq_model=jc,
mutation_rate=mutation_rate,
alphabet="DNA")
#################################
## SNJ - Jukes_Cantor
#################################
t0 = _t()
snj = spectraltree.SpectralNeighborJoining(spectraltree.JC_similarity_matrix)
sim = spectraltree.JC_similarity_matrix(observationsJC, metaJC)
inside_log = np.clip(sim, a_min=1e-16, a_max=None)
dis = -np.log(inside_log)
disC = np.array(metricNearness.metricNearness(dis))
simC = np.exp(-disC)
tree_rec = snj.reconstruct_from_similarity(sim, taxa_metadata=metaJC)
tree_recC = snj.reconstruct_from_similarity(simC, taxa_metadata=metaJC)