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Test_pedigree with internal samples #2325

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db78171
Initial test with internal samples
abureau Oct 22, 2024
fc930d8
Corrections to internal sample tests
abureau Oct 23, 2024
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22 changes: 20 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,
internal_sample_gen=(None,None,None),
) -> tskit.TableCollection:
"""
Simulates pedigree.
Expand All @@ -62,11 +63,16 @@ def simulate_pedigree(
sequence_length: The sequence_length of the output tables.
random_seed: Random seed.
"""
# Fill-in internal_sample_gen with None if shorter than number of generations
if len(internal_sample_gen) < num_generations:
tmp = internal_sample_gen
internal_sample_gen = np.repeat(None,num_generations)
internal_sample_gen[0:len(tmp)] = tmp
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)]
curr_gen = [builder.add_individual(time=time,is_sample=internal_sample_gen[0]) 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 +86,7 @@ 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=internal_sample_gen[generation])
curr_gen.append(ind_id)
return builder.finalise(sequence_length)

Expand Down Expand Up @@ -544,6 +550,18 @@ def test_shallow(self, num_founders, recombination_rate):
sequence_length=100,
)
self.verify(tables, recombination_rate)

@pytest.mark.parametrize("num_founders", [2, 3, 5, 100])
@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,
internal_sample_gen=[True, False],
)
self.verify(tables, recombination_rate)

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