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Original file line number | Diff line number | Diff line change |
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import itertools | ||
import pytest | ||
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import numpy as np | ||
import numba as nb | ||
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from . import lsbase | ||
import lshmm.core as core | ||
import lshmm.vit_haploid as vh | ||
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class TestNonTreeViterbiHaploid(lsbase.ViterbiAlgorithmBase): | ||
def verify(self, ts, include_ancestors): | ||
H, queries = self.get_examples_haploid(ts, include_ancestors) | ||
m = H.shape[0] | ||
n = H.shape[1] | ||
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r_s = [ | ||
np.append([0], np.zeros(m - 1) + 0.01), | ||
np.append([0], np.random.rand(m - 1)), | ||
np.append([0], 1e-5 * (np.random.rand(m - 1) + 0.5) / 2), | ||
np.append([0], np.zeros(m - 1) + 0.2), | ||
np.append([0], np.zeros(m - 1) + 1e-6), | ||
] | ||
mu_s = [ | ||
np.zeros(m) + 0.01, | ||
np.random.rand(m) * 0.2, | ||
1e-5 * (np.random.rand(m) + 0.5) / 2, | ||
np.zeros(m) + 0.2, | ||
np.zeros(m) + 1e-6, | ||
] | ||
kappa_s = [1 / 2, 1 / 4, 1, 3 / 2, 2] | ||
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for s, r, mu, kappa in itertools.product(queries, r_s, mu_s, kappa_s): | ||
e = core.get_emission_matrix_hkylike(mu, kappa) | ||
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V_vs, P_vs, ll_vs = vh.forwards_viterbi_hap_naive( | ||
n=n, | ||
m=m, | ||
H=H, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
path_vs = vh.backwards_viterbi_hap(m=m, V_last=V_vs[m - 1, :], P=P_vs) | ||
ll_check = vh.path_ll_hap( | ||
n=n, | ||
m=m, | ||
H=H, | ||
path=path_vs, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
self.assertAllClose(ll_vs, ll_check) | ||
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V_tmp, P_tmp, ll_tmp = vh.forwards_viterbi_hap_naive_vec( | ||
n=n, | ||
m=m, | ||
H=H, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
path_tmp = vh.backwards_viterbi_hap(m=m, V_last=V_tmp[m - 1, :], P=P_tmp) | ||
ll_check = vh.path_ll_hap( | ||
n=n, | ||
m=m, | ||
H=H, | ||
path=path_tmp, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
self.assertAllClose(ll_tmp, ll_check) | ||
self.assertAllClose(ll_vs, ll_tmp) | ||
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V_tmp, P_tmp, ll_tmp = vh.forwards_viterbi_hap_naive_low_mem( | ||
n=n, | ||
m=m, | ||
H=H, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
path_tmp = vh.backwards_viterbi_hap(m=m, V_last=V_tmp, P=P_tmp) | ||
ll_check = vh.path_ll_hap( | ||
n=n, | ||
m=m, | ||
H=H, | ||
path=path_tmp, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
self.assertAllClose(ll_tmp, ll_check) | ||
self.assertAllClose(ll_vs, ll_tmp) | ||
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V_tmp, P_tmp, ll_tmp = vh.forwards_viterbi_hap_naive_low_mem_rescaling( | ||
n=n, | ||
m=m, | ||
H=H, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
path_tmp = vh.backwards_viterbi_hap(m, V_tmp, P_tmp) | ||
ll_check = vh.path_ll_hap( | ||
n=n, | ||
m=m, | ||
H=H, | ||
path=path_tmp, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
self.assertAllClose(ll_tmp, ll_check) | ||
self.assertAllClose(ll_vs, ll_tmp) | ||
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V_tmp, P_tmp, ll_tmp = vh.forwards_viterbi_hap_low_mem_rescaling( | ||
n=n, | ||
m=m, | ||
H=H, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
path_tmp = vh.backwards_viterbi_hap(m=m, V_last=V_tmp, P=P_tmp) | ||
ll_check = vh.path_ll_hap( | ||
n=n, | ||
m=m, | ||
H=H, | ||
path=path_tmp, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
self.assertAllClose(ll_tmp, ll_check) | ||
self.assertAllClose(ll_vs, ll_tmp) | ||
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||
V_tmp, P_tmp, ll_tmp = vh.forwards_viterbi_hap_lower_mem_rescaling( | ||
n=n, | ||
m=m, | ||
H=H, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
path_tmp = vh.backwards_viterbi_hap(m, V_tmp, P_tmp) | ||
ll_check = vh.path_ll_hap( | ||
n=n, | ||
m=m, | ||
H=H, | ||
path=path_tmp, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
self.assertAllClose(ll_tmp, ll_check) | ||
self.assertAllClose(ll_vs, ll_tmp) | ||
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( | ||
V_tmp, | ||
V_argmaxes_tmp, | ||
recombs, | ||
ll_tmp, | ||
) = vh.forwards_viterbi_hap_lower_mem_rescaling_no_pointer( | ||
n=n, | ||
m=m, | ||
H=H, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
path_tmp = vh.backwards_viterbi_hap_no_pointer( | ||
m=m, | ||
V_argmaxes=V_argmaxes_tmp, | ||
recombs=nb.typed.List(recombs), | ||
) | ||
ll_check = vh.path_ll_hap( | ||
n=n, | ||
m=m, | ||
H=H, | ||
path=path_tmp, | ||
s=s, | ||
e=e, | ||
r=r, | ||
emission_func=core.get_emission_probability_haploid_hkylike, | ||
) | ||
self.assertAllClose(ll_tmp, ll_check) | ||
self.assertAllClose(ll_vs, ll_tmp) | ||
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@pytest.mark.parametrize("include_ancestors", [True, False]) | ||
def test_ts_multiallelic_n10_no_recomb(self, include_ancestors): | ||
ts = self.get_ts_multiallelic_n10_no_recomb() | ||
self.verify(ts, include_ancestors) | ||
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@pytest.mark.parametrize("num_samples", [8, 16, 32]) | ||
@pytest.mark.parametrize("include_ancestors", [True, False]) | ||
def test_ts_multiallelic(self, num_samples, include_ancestors): | ||
ts = self.get_ts_multiallelic(num_samples) | ||
self.verify(ts, include_ancestors) |