def test_allele_expectation_interface():
bgen = read_bgen(example_filepath("haplotypes.bgen"), verbose=False)
with pytest.raises(ValueError):
allele_expectation(bgen, 1)
bgen = read_bgen(example_filepath("complex.23bits.bgen"), verbose=False)
e = allele_expectation(bgen, 3)
assert_allclose(
e,
[[1.0, 0.0, 0.0], [2.0, 0.0, 0.0], [1.0, 1.0, 0.0], [0.0, 2.0, 0.0]])
def test_dosage_example_32bits():
filepath = example_filepath("example.32bits.bgen")
bgen = read_bgen(filepath, verbose=False)
e = allele_expectation(bgen, 5)
assert_allclose(e[7], [1.9556273911044997, 0.044372608895500334])
e = allele_expectation(bgen, 0)
assert all(isnan(e[0]))
e = allele_expectation(bgen, 0)
assert_equal(e.shape, (500, 2))
def test_allele_frequency_interface():
filepath = example_filepath("complex.23bits.bgen")
with pytest.raises(ValueError):
bgen = read_bgen(filepath, verbose=False)
allele_expectation(bgen, 1)
bgen = read_bgen(filepath, verbose=False)
expec = allele_expectation(bgen, 3)
freq = allele_frequency(expec)
assert_allclose(freq, [1.33333333333, 1.0, 0.0])
freq = allele_frequency([[1.0, 0.0, 0.0], [2.0, 0.0, 0.0], [1.0, 1.0, 0.0],
[0.0, 2.0, 0.0]])
assert_allclose(freq, [1.33333333333, 1.0, 0.0])
with pytest.raises(ValueError):
allele_frequency([2, 3, 1])
def test_compute_dosage():
with example_files("example.32bits.bgen") as filepath:
bgen = read_bgen(filepath, verbose=False)
variant_idx = 2
e = allele_expectation(bgen, variant_idx)
dosage = compute_dosage(e)
assert_allclose(
dosage[:5],
[
0.015502935046214363,
0.9938354277968955,
1.9793395833064196,
0.9956054727070978,
1.978790270625332,
],
)
def test_dosage_interface():
bgen = read_bgen(example_filepath("complex.23bits.bgen"), verbose=False)
e = allele_expectation(bgen, 3)
assert_allclose(compute_dosage(e), [0, 0, 0, 0])
assert_allclose(compute_dosage(e, 0), [1.0, 2.0, 1.0, 0.0])