def test_impute_with_unphased_pedigree_wild_ibd_control(self):
command = [
"-c",
"--start",
"0",
"--end",
f"{self.subsample_snp}",
"--ibd",
f"{tests_root}/test_data/[email protected]",
"--bed",
f"{tests_root}/test_data/sample_reduced@",
"--chr_range",
"1-2",
"--pedigree",
f"{tests_root}/test_data/sample.ped",
"--threads",
"2",
"--out",
f"{output_root}/test_impute_with_unphased_pedigree_control@",
]
if not self.log:
command = ["-silent_progress"] + command
args = impute.parser.parse_args(command)
impute.main(args)
coef, z, p_value = imputation_test(
[1],
imputed_prefix=
f"{output_root}/test_impute_with_unphased_pedigree_control",
expected_prefix=f"{tests_root}/test_data/sample",
start=0,
end=self.subsample_snp,
)
self.assertGreaterEqual(p_value[0], self.p_value_threshold)
self.assertGreaterEqual(p_value[1], self.p_value_threshold)
def test_impute_with_unphased_pedigree_control_backup(self):
command = [
"-c",
"--start",
"0",
"--end",
f"{self.subsample_snp}",
"--ibd",
f"{tests_root}/test_data/sample.empty",
"--bed",
f"{tests_root}/test_data/sample_reduced@",
"--chr_range",
"1-2",
"--pedigree",
f"{tests_root}/test_data/sample.ped",
"--threads",
"2",
"--out",
f"{output_root}/test_impute_with_unphased_pedigree_control_backup@",
]
if not self.log:
command = ["-silent_progress"] + command
args = impute.parser.parse_args(command)
impute.main(args)
coef, z, p_value = imputation_test(
[1],
imputed_prefix=
f"{output_root}/test_impute_with_unphased_pedigree_control_backup",
expected_prefix=f"{tests_root}/test_data/sample",
start=0,
end=self.subsample_snp,
)
def test_impute_with_unphased_king(self):
command = [
"--start",
"0",
"--end",
f"{self.subsample_snp}",
"--ibd",
f"{tests_root}/test_data/sample.our",
"--bed",
f"{tests_root}/test_data/sample_reduced@",
"--chr_range",
"1-2",
"--king",
f"{tests_root}/test_data/sample.king",
"--agesex",
f"{tests_root}/test_data/sample.agesex",
"--threads",
"2",
"--out",
f"{output_root}/test_impute_with_unphased_king@",
]
if not self.log:
command = ["-silent_progress"] + command
args = impute.parser.parse_args(command)
impute.main(args)
def test_impute_with_unphased_king_control_pca(self):
command = [
"-c",
"--start",
"0",
"--end",
f"{self.subsample_snp}",
"--ibd",
f"{tests_root}/test_data/sample.our",
"--bed",
f"{tests_root}/test_data/sample@",
"--chr_range",
"1-2",
"--king",
f"{tests_root}/test_data/sample.king",
"--agesex",
f"{tests_root}/test_data/sample.agesex",
"--pcs",
f"{tests_root}/test_data/sample1_2_pca.eigenvec",
"--pc_num",
"8",
"-find_optimal_pc",
"--threads",
"2",
"--out",
f"{output_root}/test_impute_with_unphased_king_control@",
]
if not self.log:
command = ["-silent_progress"] + command
args = impute.parser.parse_args(command)
impute.main(args)
coef, z, p_value = imputation_test(
[1, 2],
imputed_prefix=
f"{output_root}/test_impute_with_unphased_king_control",
expected_prefix=f"{tests_root}/test_data/sample",
start=0,
end=self.subsample_snp,
)
#TODO use pvals
print(coef)
self.assertAlmostEqual(coef[0], 1., delta=0.02)
self.assertAlmostEqual(coef[1], 1., delta=0.02)