def test_masked_windowed_divergence(self):
h = HaplotypeArray([[0, 0, 0, 0], [0, 0, 0, 1], [0, 0, 1, 1],
[0, 1, 1, 1], [1, 1, 1, 1], [0, 0, 1, 2],
[0, 1, 1, 2], [0, 1, -1, -1], [-1, -1, -1, -1]])
h1 = h.take([0, 1], axis=1)
h2 = h.take([2, 3], axis=1)
ac1 = h1.count_alleles()
ac2 = h2.count_alleles()
pos = SortedIndex([2, 4, 7, 14, 15, 18, 19, 25, 27])
mask = np.tile(np.repeat(np.array([True, False]), 5), 3)
expect, _, _, _ = allel.windowed_divergence(pos,
ac1,
ac2,
size=5,
start=1,
stop=31)
expect = expect[::2]
actual, _, _, _ = allel.windowed_divergence(pos,
ac1,
ac2,
size=10,
start=1,
stop=31,
is_accessible=mask)
assert_array_almost_equal(expect, actual)
def test_mean_pairwise_divergence(self):
# simplest case, two haplotypes in each population
h = HaplotypeArray([[0, 0, 0, 0], [0, 0, 0, 1], [0, 0, 1, 1],
[0, 1, 1, 1], [1, 1, 1, 1], [0, 0, 1, 2],
[0, 1, 1, 2], [0, 1, -1, -1], [-1, -1, -1, -1]])
h1 = h.take([0, 1], axis=1)
h2 = h.take([2, 3], axis=1)
ac1 = h1.count_alleles()
ac2 = h2.count_alleles()
expect = [0 / 4, 2 / 4, 4 / 4, 2 / 4, 0 / 4, 4 / 4, 3 / 4, -1, -1]
actual = allel.mean_pairwise_difference_between(ac1, ac2, fill=-1)
aeq(expect, actual)
def test_windowed_divergence(self):
# simplest case, two haplotypes in each population
h = HaplotypeArray([[0, 0, 0, 0], [0, 0, 0, 1], [0, 0, 1, 1],
[0, 1, 1, 1], [1, 1, 1, 1], [0, 0, 1, 2],
[0, 1, 1, 2], [0, 1, -1, -1], [-1, -1, -1, -1]])
h1 = h.take([0, 1], axis=1)
h2 = h.take([2, 3], axis=1)
ac1 = h1.count_alleles()
ac2 = h2.count_alleles()
# mean pairwise divergence
# expect = [0/4, 2/4, 4/4, 2/4, 0/4, 4/4, 3/4, -1, -1]
pos = SortedIndex([2, 4, 7, 14, 15, 18, 19, 25, 27])
expect = [(6 / 4) / 10, (9 / 4) / 10, 0 / 11]
actual, _, _, _ = allel.windowed_divergence(pos,
ac1,
ac2,
size=10,
start=1,
stop=31)
assert_array_almost_equal(expect, actual)