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.stats.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.stats.windowed_divergence(
pos, ac1, ac2, size=10, start=1, stop=31
)
assert_array_close(expect, actual)
