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Ls missingness #2515

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Jul 5, 2023
Merged

Ls missingness #2515

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128 changes: 83 additions & 45 deletions python/tests/test_genotype_matching_fb.py
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,4 +1,3 @@
# Simulation
import copy
import itertools

Expand All @@ -14,6 +13,8 @@
REF_HOM_OBS_HET = 1
REF_HET_OBS_HOM = 2

MISSING = -1


def mirror_coordinates(ts):
"""
Expand Down Expand Up @@ -411,6 +412,7 @@ def update_probabilities(self, site, genotype_state):
]

query_is_het = genotype_state == 1
query_is_missing = genotype_state == MISSING

for st1 in T:
u1 = st1.tree_node
Expand Down Expand Up @@ -444,6 +446,7 @@ def update_probabilities(self, site, genotype_state):
match,
template_is_het,
query_is_het,
query_is_missing,
)

# This will ensure that allelic_state[:n] is filled
Expand Down Expand Up @@ -561,7 +564,14 @@ def compute_normalisation_factor_dict(self):
raise NotImplementedError()

def compute_next_probability_dict(
self, site_id, p_last, inner_summation, is_match, template_is_het, query_is_het
self,
site_id,
p_last,
inner_summation,
is_match,
template_is_het,
query_is_het,
query_is_missing,
):
raise NotImplementedError()

Expand Down Expand Up @@ -670,41 +680,45 @@ def compute_next_probability_dict(
is_match,
template_is_het,
query_is_het,
query_is_missing,
):
rho = self.rho[site_id]
mu = self.mu[site_id]
n = self.ts.num_samples

template_is_hom = np.logical_not(template_is_het)
query_is_hom = np.logical_not(query_is_het)

EQUAL_BOTH_HOM = np.logical_and(
np.logical_and(is_match, template_is_hom), query_is_hom
)
UNEQUAL_BOTH_HOM = np.logical_and(
np.logical_and(np.logical_not(is_match), template_is_hom), query_is_hom
)
BOTH_HET = np.logical_and(template_is_het, query_is_het)
REF_HOM_OBS_HET = np.logical_and(template_is_hom, query_is_het)
REF_HET_OBS_HOM = np.logical_and(template_is_het, query_is_hom)

p_t = (
(rho / n) ** 2
+ ((1 - rho) * (rho / n)) * inner_normalisation_factor
+ (1 - rho) ** 2 * p_last
)
p_e = (
EQUAL_BOTH_HOM * (1 - mu) ** 2
+ UNEQUAL_BOTH_HOM * (mu**2)
+ REF_HOM_OBS_HET * (2 * mu * (1 - mu))
+ REF_HET_OBS_HOM * (mu * (1 - mu))
+ BOTH_HET * ((1 - mu) ** 2 + mu**2)
)

if query_is_missing:
p_e = 1
else:
query_is_hom = np.logical_not(query_is_het)
template_is_hom = np.logical_not(template_is_het)

equal_both_hom = np.logical_and(
np.logical_and(is_match, template_is_hom), query_is_hom
)
unequal_both_hom = np.logical_and(
np.logical_and(np.logical_not(is_match), template_is_hom), query_is_hom
)
both_het = np.logical_and(template_is_het, query_is_het)
ref_hom_obs_het = np.logical_and(template_is_hom, query_is_het)
ref_het_obs_hom = np.logical_and(template_is_het, query_is_hom)

p_e = (
equal_both_hom * (1 - mu) ** 2
+ unequal_both_hom * (mu**2)
+ ref_hom_obs_het * (2 * mu * (1 - mu))
+ ref_het_obs_hom * (mu * (1 - mu))
+ both_het * ((1 - mu) ** 2 + mu**2)
)

return p_t * p_e


# DEV: Sort this
class BackwardAlgorithm(LsHmmAlgorithm):
"""Runs the Li and Stephens forward algorithm."""

Expand Down Expand Up @@ -737,29 +751,35 @@ def compute_next_probability_dict(
is_match,
template_is_het,
query_is_het,
query_is_missing,
):
mu = self.mu[site_id]

template_is_hom = np.logical_not(template_is_het)
query_is_hom = np.logical_not(query_is_het)

EQUAL_BOTH_HOM = np.logical_and(
np.logical_and(is_match, template_is_hom), query_is_hom
)
UNEQUAL_BOTH_HOM = np.logical_and(
np.logical_and(np.logical_not(is_match), template_is_hom), query_is_hom
)
BOTH_HET = np.logical_and(template_is_het, query_is_het)
REF_HOM_OBS_HET = np.logical_and(template_is_hom, query_is_het)
REF_HET_OBS_HOM = np.logical_and(template_is_het, query_is_hom)

p_e = (
EQUAL_BOTH_HOM * (1 - mu) ** 2
+ UNEQUAL_BOTH_HOM * (mu**2)
+ REF_HOM_OBS_HET * (2 * mu * (1 - mu))
+ REF_HET_OBS_HOM * (mu * (1 - mu))
+ BOTH_HET * ((1 - mu) ** 2 + mu**2)
)
if query_is_missing:
p_e = 1
else:
query_is_hom = np.logical_not(query_is_het)

equal_both_hom = np.logical_and(
np.logical_and(is_match, template_is_hom), query_is_hom
)
unequal_both_hom = np.logical_and(
np.logical_and(np.logical_not(is_match), template_is_hom), query_is_hom
)
both_het = np.logical_and(template_is_het, query_is_het)
ref_hom_obs_het = np.logical_and(template_is_hom, query_is_het)
ref_het_obs_hom = np.logical_and(template_is_het, query_is_hom)

p_e = (
equal_both_hom * (1 - mu) ** 2
+ unequal_both_hom * (mu**2)
+ ref_hom_obs_het * (2 * mu * (1 - mu))
+ ref_het_obs_hom * (mu * (1 - mu))
+ both_het * ((1 - mu) ** 2 + mu**2)
)

return p_next * p_e


Expand Down Expand Up @@ -797,18 +817,33 @@ def example_genotypes(self, ts):
s = H[:, 0].reshape(1, H.shape[0]) + H[:, 1].reshape(1, H.shape[0])
H = H[:, 2:]

genotypes = [
s,
H[:, -1].reshape(1, H.shape[0]) + H[:, -2].reshape(1, H.shape[0]),
]

s_tmp = s.copy()
s_tmp[0, -1] = MISSING
genotypes.append(s_tmp)
s_tmp = s.copy()
s_tmp[0, ts.num_sites // 2] = MISSING
genotypes.append(s_tmp)
s_tmp = s.copy()
s_tmp[0, :] = MISSING
genotypes.append(s_tmp)

m = ts.get_num_sites()
n = H.shape[1]

G = np.zeros((m, n, n))
for i in range(m):
G[i, :, :] = np.add.outer(H[i, :], H[i, :])

return H, G, s
return H, G, genotypes

def example_parameters_genotypes(self, ts, seed=42):
np.random.seed(seed)
H, G, s = self.example_genotypes(ts)
H, G, genotypes = self.example_genotypes(ts)
n = H.shape[1]
m = ts.get_num_sites()

Expand All @@ -819,13 +854,16 @@ def example_parameters_genotypes(self, ts, seed=42):

e = self.genotype_emission(mu, m)

yield n, m, G, s, e, r, mu
for s in genotypes:
yield n, m, G, s, e, r, mu

# Mixture of random and extremes
rs = [np.zeros(m) + 0.999, np.zeros(m) + 1e-6, np.random.rand(m)]
mus = [np.zeros(m) + 0.33, np.zeros(m) + 1e-6, np.random.rand(m) * 0.33]

for r, mu in itertools.product(rs, mus):
e = self.genotype_emission(mu, m)

for s, r, mu in itertools.product(genotypes, rs, mus):
r[0] = 0
e = self.genotype_emission(mu, m)
yield n, m, G, s, e, r, mu
Expand Down
74 changes: 50 additions & 24 deletions python/tests/test_genotype_matching_viterbi.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,8 @@
REF_HOM_OBS_HET = 1
REF_HET_OBS_HOM = 2

MISSING = -1


class ValueTransition:
"""Simple struct holding value transition values."""
Expand Down Expand Up @@ -390,6 +392,7 @@ def update_probabilities(self, site, genotype_state):
]

query_is_het = genotype_state == 1
query_is_missing = genotype_state == MISSING

for st1 in T:
u1 = st1.tree_node
Expand Down Expand Up @@ -423,6 +426,7 @@ def update_probabilities(self, site, genotype_state):
match,
template_is_het,
query_is_het,
query_is_missing,
u1,
u2,
)
Expand Down Expand Up @@ -486,6 +490,7 @@ def compute_next_probability_dict(
is_match,
template_is_het,
query_is_het,
query_is_missing,
node_1,
node_2,
):
Expand Down Expand Up @@ -830,6 +835,7 @@ def compute_next_probability_dict(
is_match,
template_is_het,
query_is_het,
query_is_missing,
node_1,
node_2,
):
Expand All @@ -841,26 +847,28 @@ def compute_next_probability_dict(
double_recombination_required = False
single_recombination_required = False

template_is_hom = np.logical_not(template_is_het)
query_is_hom = np.logical_not(query_is_het)

EQUAL_BOTH_HOM = np.logical_and(
np.logical_and(is_match, template_is_hom), query_is_hom
)
UNEQUAL_BOTH_HOM = np.logical_and(
np.logical_and(np.logical_not(is_match), template_is_hom), query_is_hom
)
BOTH_HET = np.logical_and(template_is_het, query_is_het)
REF_HOM_OBS_HET = np.logical_and(template_is_hom, query_is_het)
REF_HET_OBS_HOM = np.logical_and(template_is_het, query_is_hom)

p_e = (
EQUAL_BOTH_HOM * (1 - mu) ** 2
+ UNEQUAL_BOTH_HOM * (mu**2)
+ REF_HOM_OBS_HET * (2 * mu * (1 - mu))
+ REF_HET_OBS_HOM * (mu * (1 - mu))
+ BOTH_HET * ((1 - mu) ** 2 + mu**2)
)
if query_is_missing:
p_e = 1
else:
template_is_hom = np.logical_not(template_is_het)
query_is_hom = np.logical_not(query_is_het)
equal_both_hom = np.logical_and(
np.logical_and(is_match, template_is_hom), query_is_hom
)
unequal_both_hom = np.logical_and(
np.logical_and(np.logical_not(is_match), template_is_hom), query_is_hom
)
both_het = np.logical_and(template_is_het, query_is_het)
ref_hom_obs_het = np.logical_and(template_is_hom, query_is_het)
ref_het_obs_hom = np.logical_and(template_is_het, query_is_hom)

p_e = (
equal_both_hom * (1 - mu) ** 2
+ unequal_both_hom * (mu**2)
+ ref_hom_obs_het * (2 * mu * (1 - mu))
+ ref_het_obs_hom * (mu * (1 - mu))
+ both_het * ((1 - mu) ** 2 + mu**2)
)

no_switch = (1 - r) ** 2 + 2 * (r_n * (1 - r)) + r_n**2
single_switch = r_n * (1 - r) + r_n**2
Expand Down Expand Up @@ -919,18 +927,33 @@ def example_genotypes(self, ts):
s = H[:, 0].reshape(1, H.shape[0]) + H[:, 1].reshape(1, H.shape[0])
H = H[:, 2:]

genotypes = [
s,
H[:, -1].reshape(1, H.shape[0]) + H[:, -2].reshape(1, H.shape[0]),
]

s_tmp = s.copy()
s_tmp[0, -1] = MISSING
genotypes.append(s_tmp)
s_tmp = s.copy()
s_tmp[0, ts.num_sites // 2] = MISSING
genotypes.append(s_tmp)
s_tmp = s.copy()
s_tmp[0, :] = MISSING
genotypes.append(s_tmp)

m = ts.get_num_sites()
n = H.shape[1]

G = np.zeros((m, n, n))
for i in range(m):
G[i, :, :] = np.add.outer(H[i, :], H[i, :])

return H, G, s
return H, G, genotypes

def example_parameters_genotypes(self, ts, seed=42):
np.random.seed(seed)
H, G, s = self.example_genotypes(ts)
H, G, genotypes = self.example_genotypes(ts)
n = H.shape[1]
m = ts.get_num_sites()

Expand All @@ -941,13 +964,16 @@ def example_parameters_genotypes(self, ts, seed=42):

e = self.genotype_emission(mu, m)

yield n, m, G, s, e, r, mu
for s in genotypes:
yield n, m, G, s, e, r, mu

# Mixture of random and extremes
rs = [np.zeros(m) + 0.999, np.zeros(m) + 1e-6, np.random.rand(m)]
mus = [np.zeros(m) + 0.33, np.zeros(m) + 1e-6, np.random.rand(m) * 0.33]

for r, mu in itertools.product(rs, mus):
e = self.genotype_emission(mu, m)

for s, r, mu in itertools.product(genotypes, rs, mus):
r[0] = 0
e = self.genotype_emission(mu, m)
yield n, m, G, s, e, r, mu
Expand Down