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Merged
jeromekelleher merged 2 commits into from
Jul 24, 2025
Merged

Test_pedigree.py with internal samples #2326

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188d1ec
Initial test with internal samples
abureau Oct 22, 2024
78255b6
Update the tests and API
jeromekelleher Jul 24, 2025
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26 changes: 24 additions & 2 deletions tests/test_pedigree.py
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Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@ def simulate_pedigree(
num_generations=3,
sequence_length=1,
random_seed=42,
sample_gen=None,
) -> tskit.TableCollection:
"""
Simulates pedigree.
Expand All @@ -61,12 +62,19 @@ def simulate_pedigree(
num_generations: Number of generations to attempt to simulate
sequence_length: The sequence_length of the output tables.
random_seed: Random seed.
sample_gen: Generations at which all individuals are samples. Defaults
to the first generation (backwards in time).
"""
rng = np.random.RandomState(random_seed)
builder = msprime.PedigreeBuilder()

time = num_generations - 1
curr_gen = [builder.add_individual(time=time) for _ in range(num_founders)]
if sample_gen is None:
sample_gen = [0]
curr_gen = [
builder.add_individual(time=time, is_sample=time in sample_gen)
for _ in range(num_founders)
]
for generation in range(1, num_generations):
num_pairs = len(curr_gen) // 2
if num_pairs == 0 and num_children_prob[0] != 1:
Expand All @@ -80,7 +88,9 @@ def simulate_pedigree(
num_children = rng.choice(len(num_children_prob), p=num_children_prob)
for _ in range(num_children):
parents = np.sort(parents).astype(np.int32)
ind_id = builder.add_individual(time=time, parents=parents)
ind_id = builder.add_individual(
time=time, parents=parents, is_sample=time in sample_gen
)
curr_gen.append(ind_id)
return builder.finalise(sequence_length)

Expand Down Expand Up @@ -545,6 +555,18 @@ def test_shallow(self, num_founders, recombination_rate):
)
self.verify(tables, recombination_rate)

@pytest.mark.parametrize("num_founders", [2, 3, 5])
@pytest.mark.parametrize("recombination_rate", [0, 0.01])
def test_shallow_internal(self, num_founders, recombination_rate):
tables = simulate_pedigree(
num_founders=num_founders,
num_children_prob=[0, 0, 1],
num_generations=2,
sequence_length=100,
sample_gen=[0, 1],
)
self.verify(tables, recombination_rate)

@pytest.mark.parametrize("num_founders", [2, 3, 10, 20])
@pytest.mark.parametrize("recombination_rate", [0, 0.01])
def test_deep(self, num_founders, recombination_rate):
Expand Down
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