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))