def test_homalt_homalt(self):
parents = np.hstack([self.halt_parent, self.halt_parent])
non_mendelian = diploid_mendelian_error_biallelic(
parental_genotypes=parents,
progeny_genotypes=self.progeny
)
self.assertTrue(np.array_equal(non_mendelian[0], [2, 1, 0, 0]))
def test_multiple_variants(self):
parents = np.vstack([np.hstack([self.href_parent, self.href_parent]),
np.hstack([self.halt_parent, self.halt_parent]),
np.hstack([self.het_parent, self.halt_parent]),
np.hstack([self.het_parent, self.het_parent])])
multiv_progeny = np.repeat(self.progeny, 4, axis=0)
non_mendelian = diploid_mendelian_error_biallelic(
parental_genotypes=parents,
progeny_genotypes=multiv_progeny
)
expected_result = np.array([[0, 1, 2, 0],
[2, 1, 0, 0],
[1, 0, 0, 0],
[0, 0, 0, 0]])
self.assertTrue(np.array_equal(parents.shape, (4, 2, 2)))
self.assertTrue(np.array_equal(non_mendelian.shape,
expected_result.shape))
self.assertTrue(np.array_equal(non_mendelian, expected_result))
