def test_genotype_temp_files_removed_in_server_side(self):
# Prepare
shutil.rmtree('/tmp/ukbrest2tmp/', ignore_errors=True)
genoq = GenoQuery(get_repository_path('example01'),
tmpdir='/tmp/ukbrest2tmp/')
# Configure
app.app.config['TESTING'] = True
app.app.config['genoquery'] = genoq
test_client = app.app.test_client()
# Run
response = test_client.get(
'/ukbrest/api/v1.0/genotype/1/positions/100/276')
# Validate
assert response.status_code == 200, response.status_code
bgen_file = self._save_file(response)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 3
assert os.path.isdir('/tmp/ukbrest2tmp/')
assert len(os.listdir('/tmp/ukbrest2tmp/')) == 0
def test_genotype_rsids_using_file_http_auth_with_credentials(self):
# Prepare
self.setUp(user_pass_line='user: thepassword2')
rsids_file = get_repository_path('example01/rsids01.txt')
# Run
response = self.app.post(
'/ukbrest/api/v1.0/genotype/2/rsids',
data={'file': (open(rsids_file, 'rb'), rsids_file)},
headers=self._get_http_basic_auth_header('user', 'thepassword2'),
)
# Validate
assert response.status_code == 200, response.status_code
bgen_file = self._save_file(response)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 5
def test_query_incl_range_upper_limit_only(self):
# prepare
genoq = GenoQuery(get_repository_path('example01'))
# run
bgen_file = genoq.get_incl_range(chr=1, stop=276)
# validate
assert bgen_file is not None
assert isfile(bgen_file)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 3
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 3
assert results.loc[0, 'rsid'] == 'rs1'
assert results.loc[1, 'rsid'] == 'rs2'
assert results.loc[2, 'rsid'] == 'rs3'
assert results.loc[0, 'allele1'] == 'G'
assert results.loc[0, 'allele2'] == 'A'
assert results.loc[1, 'allele1'] == 'G'
assert results.loc[1, 'allele2'] == 'C'
assert results.loc[2, 'allele1'] == 'C'
assert results.loc[2, 'allele2'] == 'A'
assert results.loc[0, '1.aa'] == 0.7491
assert results.loc[0, '1.ab'] == 0.0133
assert results.loc[0, '1.bb'] == 0.2376
assert results.loc[1, '2.aa'] == 0.8654
assert results.loc[1, '2.ab'] == 0.1041
assert results.loc[1, '2.bb'] == 0.0306
assert results.loc[2, '300.aa'] == 0.0828
assert results.loc[2, '300.ab'] == 0.7752
assert results.loc[2, '300.bb'] == 0.1421
pos_values = results['pos'].unique()
assert len(pos_values) == 3
assert results.loc[0, 'pos'] == 100
assert results.loc[1, 'pos'] == 181
assert results.loc[2, 'pos'] == 276
def test_genotype_positions_lower_and_upper_limits(self):
# Prepare
# Run
response = self.app.get(
'/ukbrest/api/v1.0/genotype/1/positions/100/276')
# Validate
assert response.status_code == 200, response.status_code
bgen_file = self._save_file(response)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 3
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 3
assert results.loc[0, 'rsid'] == 'rs1'
assert results.loc[1, 'rsid'] == 'rs2'
assert results.loc[2, 'rsid'] == 'rs3'
assert results.loc[0, 'allele1'] == 'G'
assert results.loc[0, 'allele2'] == 'A'
assert results.loc[1, 'allele1'] == 'G'
assert results.loc[1, 'allele2'] == 'C'
assert results.loc[2, 'allele1'] == 'C'
assert results.loc[2, 'allele2'] == 'A'
assert results.loc[0, '1.aa'] == 0.7491
assert results.loc[0, '1.ab'] == 0.0133
assert results.loc[0, '1.bb'] == 0.2376
assert results.loc[1, '2.aa'] == 0.8654
assert results.loc[1, '2.ab'] == 0.1041
assert results.loc[1, '2.bb'] == 0.0306
assert results.loc[2, '300.aa'] == 0.0828
assert results.loc[2, '300.ab'] == 0.7752
assert results.loc[2, '300.bb'] == 0.1421
pos_values = results['pos'].unique()
assert len(pos_values) == 3
assert results.loc[0, 'pos'] == 100
assert results.loc[1, 'pos'] == 181
assert results.loc[2, 'pos'] == 276
def test_query_incl_rsids_multiple(self):
# prepare
genoq = GenoQuery(get_repository_path('example01'))
# run
bgen_file = genoq.get_incl_rsids(2, ['rs2000082', 'rs2000142'])
# validate
assert bgen_file is not None
assert isfile(bgen_file)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 2
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 2
assert results.loc[0, 'rsid'] == 'rs2000082'
assert results.loc[1, 'rsid'] == 'rs2000142'
assert results.loc[0, 'allele1'] == 'A'
assert results.loc[0, 'allele2'] == 'T'
assert results.loc[1, 'allele1'] == 'T'
assert results.loc[1, 'allele2'] == 'G'
assert results.loc[0, '1.aa'] == 0.0016
assert results.loc[0, '1.ab'] == 0.8613
assert results.loc[0, '1.bb'] == 0.1371
assert results.loc[0, '300.aa'] == 0.0234
assert results.loc[0, '300.ab'] == 0.0148
assert results.loc[0, '300.bb'] == 0.9618
assert results.loc[1, '1.aa'] == 0.9619
assert results.loc[1, '1.ab'] == 0.0015
assert results.loc[1, '1.bb'] == 0.0366
assert results.loc[1, '300.aa'] == 0.0185
assert results.loc[1, '300.ab'] == 0.1408
assert results.loc[1, '300.bb'] == 0.8407
pos_values = results['pos'].unique()
assert len(pos_values) == 2
assert results.loc[0, 'pos'] == 6192
assert results.loc[1, 'pos'] == 10750
def test_query_incl_range_temp_directory(self):
# prepare
shutil.rmtree('/tmp/ukbrest_different/', ignore_errors=True)
genoq = GenoQuery(get_repository_path('example01'),
tmpdir='/tmp/ukbrest_different/')
# run
bgen_file = genoq.get_incl_range(chr=1, start=100, stop=276)
# validate
assert bgen_file is not None
assert isfile(bgen_file)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 3
assert isdir('/tmp/ukbrest_different/')
assert len(os.listdir('/tmp/ukbrest_different/')) == 1
def test_genotype_positions_lower_and_upper_limits_http_auth_with_credentials(
self):
# Prepare
self.setUp(user_pass_line='user: thepassword2')
# Run
response = self.app.get(
'/ukbrest/api/v1.0/genotype/1/positions/100/276',
headers=self._get_http_basic_auth_header('user', 'thepassword2'),
)
# Validate
assert response.status_code == 200, response.status_code
bgen_file = self._save_file(response)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 3
def test_query_incl_range_lower_and_upper_limits_at_end(self):
# prepare
genoq = GenoQuery(get_repository_path('example01'))
# run
bgen_file = genoq.get_incl_range(chr=1, start=18058, stop=18389)
# validate
assert bgen_file is not None
assert isfile(bgen_file)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 5
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 5
assert results.loc[0, 'rsid'] == 'rs246'
assert results.loc[1, 'rsid'] == 'rs247'
assert results.loc[2, 'rsid'] == 'rs248'
assert results.loc[3, 'rsid'] == 'rs249'
assert results.loc[4, 'rsid'] == 'rs250'
assert results.loc[0, 'allele1'] == 'C'
assert results.loc[0, 'allele2'] == 'A'
assert results.loc[1, 'allele1'] == 'T'
assert results.loc[1, 'allele2'] == 'C'
assert results.loc[2, 'allele1'] == 'G'
assert results.loc[2, 'allele2'] == 'C'
assert results.loc[3, 'allele1'] == 'G'
assert results.loc[3, 'allele2'] == 'A'
assert results.loc[4, 'allele1'] == 'T'
assert results.loc[4, 'allele2'] == 'C'
assert results.loc[0, '1.aa'] == 0.0537
assert results.loc[0, '1.ab'] == 0.9160
assert results.loc[0, '1.bb'] == 0.0302
assert results.loc[1, '2.aa'] == 0.0698
assert results.loc[1, '2.ab'] == 0.9116
assert results.loc[1, '2.bb'] == 0.0186
assert results.loc[2, '300.aa'] == 0.0826
assert results.loc[2, '300.ab'] == 0.0316
assert results.loc[2, '300.bb'] == 0.8858
assert results.loc[3, '299.aa'] == 0.7988
assert results.loc[3, '299.ab'] == 0.1666
assert results.loc[3, '299.bb'] == 0.0346
assert results.loc[4, '150.aa'] == 0.0773
assert results.loc[4, '150.ab'] == 0.8683
assert results.loc[4, '150.bb'] == 0.0544
pos_values = results['pos'].unique()
assert len(pos_values) == 5
assert results.loc[0, 'pos'] == 18058
assert results.loc[1, 'pos'] == 18139
assert results.loc[2, 'pos'] == 18211
assert results.loc[3, 'pos'] == 18294
assert results.loc[4, 'pos'] == 18389
def test_query_incl_rsids_using_file(self):
# prepare
genoq = GenoQuery(get_repository_path('example01'))
# rsids are not ordered in the file, but they should be returned ordered
rsids_file = get_repository_path('example01/rsids01.txt')
# run
bgen_file = genoq.get_incl_rsids(2, [rsids_file])
# validate
assert bgen_file is not None
assert isfile(bgen_file)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 5
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 5
assert results.loc[0, 'rsid'] == 'rs2000000'
assert results.loc[1, 'rsid'] == 'rs2000020'
assert results.loc[2, 'rsid'] == 'rs2000079'
assert results.loc[3, 'rsid'] == 'rs2000138'
assert results.loc[4, 'rsid'] == 'rs2000149'
assert results.loc[0, 'allele1'] == 'A'
assert results.loc[0, 'allele2'] == 'G'
assert results.loc[1, 'allele1'] == 'G'
assert results.loc[1, 'allele2'] == 'C'
assert results.loc[2, 'allele1'] == 'C'
assert results.loc[2, 'allele2'] == 'A'
assert results.loc[3, 'allele1'] == 'A'
assert results.loc[3, 'allele2'] == 'G'
assert results.loc[4, 'allele1'] == 'G'
assert results.loc[4, 'allele2'] == 'T'
assert results.loc[0, '1.aa'] == 0.9440
assert results.loc[0, '1.ab'] == 0.0298
assert results.loc[0, '1.bb'] == 0.0262
assert results.loc[1, '2.aa'] == 0.1534
assert results.loc[1, '2.ab'] == 0.7249
assert results.loc[1, '2.bb'] == 0.1218
assert results.loc[2, '3.aa'] == 0.9357
assert results.loc[2, '3.ab'] == 0.0047
assert results.loc[2, '3.bb'] == 0.0596
assert results.loc[3, '1.aa'] == 0.8246
assert results.loc[3, '1.ab'] == 0.0686
assert results.loc[3, '1.bb'] == 0.1068
assert results.loc[4, '2.aa'] == 0.0137
assert results.loc[4, '2.ab'] == 0.0953
assert results.loc[4, '2.bb'] == 0.8909
pos_values = results['pos'].unique()
assert len(pos_values) == 5
assert results.loc[0, 'pos'] == 100
assert results.loc[1, 'pos'] == 1623
assert results.loc[2, 'pos'] == 5925
assert results.loc[3, 'pos'] == 10447
assert results.loc[4, 'pos'] == 11226
def test_query_incl_range_using_file(self):
# prepare
genoq = GenoQuery(get_repository_path('example01'))
# positions are not ordered in the file, but they should be returned ordered
positions_file = get_repository_path('example01/positions01.txt')
# run
bgen_file = genoq.get_incl_range_from_file(2, positions_file)
# validate
assert bgen_file is not None
assert isfile(bgen_file)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 5
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 5
assert results.loc[0, 'rsid'] == 'rs2000003'
assert results.loc[1, 'rsid'] == 'rs2000008'
assert results.loc[2, 'rsid'] == 'rs2000094'
assert results.loc[3, 'rsid'] == 'rs2000118'
assert results.loc[4, 'rsid'] == 'rs2000149'
assert results.loc[0, 'allele1'] == 'C'
assert results.loc[0, 'allele2'] == 'G'
assert results.loc[1, 'allele1'] == 'T'
assert results.loc[1, 'allele2'] == 'A'
assert results.loc[2, 'allele1'] == 'C'
assert results.loc[2, 'allele2'] == 'G'
assert results.loc[3, 'allele1'] == 'T'
assert results.loc[3, 'allele2'] == 'C'
assert results.loc[4, 'allele1'] == 'G'
assert results.loc[4, 'allele2'] == 'T'
assert results.loc[0, '1.aa'] == 0.7889
assert results.loc[0, '1.ab'] == 0.1538
assert results.loc[0, '1.bb'] == 0.0573
assert results.loc[1, '2.aa'] == 0.8776
assert results.loc[1, '2.ab'] == 0.0670
assert results.loc[1, '2.bb'] == 0.0554
assert results.loc[2, '3.aa'] == 0.0553
assert results.loc[2, '3.ab'] == 0.0939
assert results.loc[2, '3.bb'] == 0.8509
assert results.loc[3, '1.aa'] == 0.1219
assert results.loc[3, '1.ab'] == 0.8459
assert results.loc[3, '1.bb'] == 0.0323
assert results.loc[4, '2.aa'] == 0.0137
assert results.loc[4, '2.ab'] == 0.0953
assert results.loc[4, '2.bb'] == 0.8909
pos_values = results['pos'].unique()
assert len(pos_values) == 5
assert results.loc[0, 'pos'] == 300
assert results.loc[1, 'pos'] == 661
assert results.loc[2, 'pos'] == 7181
assert results.loc[3, 'pos'] == 8949
assert results.loc[4, 'pos'] == 11226
def test_genotype_positions_different_file_naming_chr2(self):
# Prepare
data_dir = get_repository_path('example02')
if os.path.isdir(data_dir):
shutil.rmtree(data_dir)
shutil.copytree(get_repository_path('example01'), data_dir)
shutil.move(os.path.join(data_dir, 'chr1impv1.bgen'),
os.path.join(data_dir, 'ukb_chr1.bgen'))
shutil.move(os.path.join(data_dir, 'chr1impv1.bgen.bgi'),
os.path.join(data_dir, 'ukb_chr1.bgen.bgi'))
shutil.move(os.path.join(data_dir, 'chr2impv1.bgen'),
os.path.join(data_dir, 'ukb_chr2.bgen'))
shutil.move(os.path.join(data_dir, 'chr2impv1.bgen.bgi'),
os.path.join(data_dir, 'ukb_chr2.bgen.bgi'))
shutil.move(os.path.join(data_dir, 'chr3impv1.bgen'),
os.path.join(data_dir, 'ukb_chr3.bgen'))
shutil.move(os.path.join(data_dir, 'chr3impv1.bgen.bgi'),
os.path.join(data_dir, 'ukb_chr3.bgen.bgi'))
self.setUp(data_dir='example02', bgen_names='ukb_chr{:d}.bgen')
positions_file = get_repository_path('example02/positions01.txt')
# Run
response = self.app.post(
'/ukbrest/api/v1.0/genotype/2/positions',
data={'file': (open(positions_file, 'rb'), positions_file)})
# Validate
assert response.status_code == 200, response.status_code
bgen_file = self._save_file(response)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 5
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 5
assert results.loc[0, 'rsid'] == 'rs2000003'
assert results.loc[1, 'rsid'] == 'rs2000008'
assert results.loc[2, 'rsid'] == 'rs2000094'
assert results.loc[3, 'rsid'] == 'rs2000118'
assert results.loc[4, 'rsid'] == 'rs2000149'
assert results.loc[0, 'allele1'] == 'C'
assert results.loc[0, 'allele2'] == 'G'
assert results.loc[1, 'allele1'] == 'T'
assert results.loc[1, 'allele2'] == 'A'
assert results.loc[2, 'allele1'] == 'C'
assert results.loc[2, 'allele2'] == 'G'
assert results.loc[3, 'allele1'] == 'T'
assert results.loc[3, 'allele2'] == 'C'
assert results.loc[4, 'allele1'] == 'G'
assert results.loc[4, 'allele2'] == 'T'
assert results.loc[0, '1.aa'] == 0.7889
assert results.loc[0, '1.ab'] == 0.1538
assert results.loc[0, '1.bb'] == 0.0573
assert results.loc[1, '2.aa'] == 0.8776
assert results.loc[1, '2.ab'] == 0.0670
assert results.loc[1, '2.bb'] == 0.0554
assert results.loc[2, '3.aa'] == 0.0553
assert results.loc[2, '3.ab'] == 0.0939
assert results.loc[2, '3.bb'] == 0.8509
assert results.loc[3, '1.aa'] == 0.1219
assert results.loc[3, '1.ab'] == 0.8459
assert results.loc[3, '1.bb'] == 0.0323
assert results.loc[4, '2.aa'] == 0.0137
assert results.loc[4, '2.ab'] == 0.0953
assert results.loc[4, '2.bb'] == 0.8909
pos_values = results['pos'].unique()
assert len(pos_values) == 5
assert results.loc[0, 'pos'] == 300
assert results.loc[1, 'pos'] == 661
assert results.loc[2, 'pos'] == 7181
assert results.loc[3, 'pos'] == 8949
assert results.loc[4, 'pos'] == 11226
shutil.rmtree(data_dir)
def test_genotype_positions_different_file_naming_chr1(self):
# Prepare
data_dir = get_repository_path('example02')
if os.path.isdir(data_dir):
shutil.rmtree(data_dir)
shutil.copytree(get_repository_path('example01'), data_dir)
shutil.move(os.path.join(data_dir, 'chr1impv1.bgen'),
os.path.join(data_dir, 'ukb_chr1.bgen'))
shutil.move(os.path.join(data_dir, 'chr1impv1.bgen.bgi'),
os.path.join(data_dir, 'ukb_chr1.bgen.bgi'))
shutil.move(os.path.join(data_dir, 'chr2impv1.bgen'),
os.path.join(data_dir, 'ukb_chr2.bgen'))
shutil.move(os.path.join(data_dir, 'chr2impv1.bgen.bgi'),
os.path.join(data_dir, 'ukb_chr2.bgen.bgi'))
shutil.move(os.path.join(data_dir, 'chr3impv1.bgen'),
os.path.join(data_dir, 'ukb_chr3.bgen'))
shutil.move(os.path.join(data_dir, 'chr3impv1.bgen.bgi'),
os.path.join(data_dir, 'ukb_chr3.bgen.bgi'))
self.setUp(data_dir='example02', bgen_names='ukb_chr1.bgen')
# Run
response = self.app.get(
'/ukbrest/api/v1.0/genotype/1/positions/100/276')
# Validate
assert response.status_code == 200, response.status_code
bgen_file = self._save_file(response)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 3
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 3
assert results.loc[0, 'rsid'] == 'rs1'
assert results.loc[1, 'rsid'] == 'rs2'
assert results.loc[2, 'rsid'] == 'rs3'
assert results.loc[0, 'allele1'] == 'G'
assert results.loc[0, 'allele2'] == 'A'
assert results.loc[1, 'allele1'] == 'G'
assert results.loc[1, 'allele2'] == 'C'
assert results.loc[2, 'allele1'] == 'C'
assert results.loc[2, 'allele2'] == 'A'
assert results.loc[0, '1.aa'] == 0.7491
assert results.loc[0, '1.ab'] == 0.0133
assert results.loc[0, '1.bb'] == 0.2376
assert results.loc[1, '2.aa'] == 0.8654
assert results.loc[1, '2.ab'] == 0.1041
assert results.loc[1, '2.bb'] == 0.0306
assert results.loc[2, '300.aa'] == 0.0828
assert results.loc[2, '300.ab'] == 0.7752
assert results.loc[2, '300.bb'] == 0.1421
pos_values = results['pos'].unique()
assert len(pos_values) == 3
assert results.loc[0, 'pos'] == 100
assert results.loc[1, 'pos'] == 181
assert results.loc[2, 'pos'] == 276
shutil.rmtree(data_dir)
def test_genotype_rsids_one_rsid_not_found(self):
# Prepare
rsids_file = get_repository_path('example01/rsids01_bug1.txt')
# Run
response = self.app.post(
'/ukbrest/api/v1.0/genotype/2/rsids',
data={'file': (open(rsids_file, 'rb'), rsids_file)})
# Validate
assert response.status_code == 200, response.status_code
bgen_file = self._save_file(response)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 4
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 4
assert results.loc[0, 'rsid'] == 'rs2000000'
assert results.loc[1, 'rsid'] == 'rs2000020'
assert results.loc[2, 'rsid'] == 'rs2000138'
assert results.loc[3, 'rsid'] == 'rs2000149'
assert results.loc[0, 'allele1'] == 'A'
assert results.loc[0, 'allele2'] == 'G'
assert results.loc[1, 'allele1'] == 'G'
assert results.loc[1, 'allele2'] == 'C'
assert results.loc[2, 'allele1'] == 'A'
assert results.loc[2, 'allele2'] == 'G'
assert results.loc[3, 'allele1'] == 'G'
assert results.loc[3, 'allele2'] == 'T'
assert results.loc[0, '1.aa'] == 0.9440
assert results.loc[0, '1.ab'] == 0.0298
assert results.loc[0, '1.bb'] == 0.0262
assert results.loc[1, '2.aa'] == 0.1534
assert results.loc[1, '2.ab'] == 0.7249
assert results.loc[1, '2.bb'] == 0.1218
assert results.loc[2, '1.aa'] == 0.8246
assert results.loc[2, '1.ab'] == 0.0686
assert results.loc[2, '1.bb'] == 0.1068
assert results.loc[3, '2.aa'] == 0.0137
assert results.loc[3, '2.ab'] == 0.0953
assert results.loc[3, '2.bb'] == 0.8909
pos_values = results['pos'].unique()
assert len(pos_values) == 4
assert results.loc[0, 'pos'] == 100
assert results.loc[1, 'pos'] == 1623
assert results.loc[2, 'pos'] == 10447
assert results.loc[3, 'pos'] == 11226
def test_genotype_positions_using_file(self):
# Prepare
positions_file = get_repository_path('example01/positions01.txt')
# Run
response = self.app.post(
'/ukbrest/api/v1.0/genotype/2/positions',
data={'file': (open(positions_file, 'rb'), positions_file)})
# Validate
assert response.status_code == 200, response.status_code
bgen_file = self._save_file(response)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 5
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 5
assert results.loc[0, 'rsid'] == 'rs2000003'
assert results.loc[1, 'rsid'] == 'rs2000008'
assert results.loc[2, 'rsid'] == 'rs2000094'
assert results.loc[3, 'rsid'] == 'rs2000118'
assert results.loc[4, 'rsid'] == 'rs2000149'
assert results.loc[0, 'allele1'] == 'C'
assert results.loc[0, 'allele2'] == 'G'
assert results.loc[1, 'allele1'] == 'T'
assert results.loc[1, 'allele2'] == 'A'
assert results.loc[2, 'allele1'] == 'C'
assert results.loc[2, 'allele2'] == 'G'
assert results.loc[3, 'allele1'] == 'T'
assert results.loc[3, 'allele2'] == 'C'
assert results.loc[4, 'allele1'] == 'G'
assert results.loc[4, 'allele2'] == 'T'
assert results.loc[0, '1.aa'] == 0.7889
assert results.loc[0, '1.ab'] == 0.1538
assert results.loc[0, '1.bb'] == 0.0573
assert results.loc[1, '2.aa'] == 0.8776
assert results.loc[1, '2.ab'] == 0.0670
assert results.loc[1, '2.bb'] == 0.0554
assert results.loc[2, '3.aa'] == 0.0553
assert results.loc[2, '3.ab'] == 0.0939
assert results.loc[2, '3.bb'] == 0.8509
assert results.loc[3, '1.aa'] == 0.1219
assert results.loc[3, '1.ab'] == 0.8459
assert results.loc[3, '1.bb'] == 0.0323
assert results.loc[4, '2.aa'] == 0.0137
assert results.loc[4, '2.ab'] == 0.0953
assert results.loc[4, '2.bb'] == 0.8909
pos_values = results['pos'].unique()
assert len(pos_values) == 5
assert results.loc[0, 'pos'] == 300
assert results.loc[1, 'pos'] == 661
assert results.loc[2, 'pos'] == 7181
assert results.loc[3, 'pos'] == 8949
assert results.loc[4, 'pos'] == 11226
def test_genotype_positions_lower_limit_only(self):
# Prepare
# Run
response = self.app.get('/ukbrest/api/v1.0/genotype/1/positions/18058')
# Validate
assert response.status_code == 200, response.status_code
bgen_file = self._save_file(response)
results = qctool(bgen_file)
assert results is not None
assert hasattr(results, 'shape')
assert hasattr(results, 'columns')
assert results.shape[1] == 6 + 300 * 3
assert results.shape[0] == 5
rsid_values = results['rsid'].unique()
assert len(rsid_values) == 5
assert results.loc[0, 'rsid'] == 'rs246'
assert results.loc[1, 'rsid'] == 'rs247'
assert results.loc[2, 'rsid'] == 'rs248'
assert results.loc[3, 'rsid'] == 'rs249'
assert results.loc[4, 'rsid'] == 'rs250'
assert results.loc[0, 'allele1'] == 'C'
assert results.loc[0, 'allele2'] == 'A'
assert results.loc[1, 'allele1'] == 'T'
assert results.loc[1, 'allele2'] == 'C'
assert results.loc[2, 'allele1'] == 'G'
assert results.loc[2, 'allele2'] == 'C'
assert results.loc[3, 'allele1'] == 'G'
assert results.loc[3, 'allele2'] == 'A'
assert results.loc[4, 'allele1'] == 'T'
assert results.loc[4, 'allele2'] == 'C'
assert results.loc[0, '1.aa'] == 0.0537
assert results.loc[0, '1.ab'] == 0.9160
assert results.loc[0, '1.bb'] == 0.0302
assert results.loc[1, '2.aa'] == 0.0698
assert results.loc[1, '2.ab'] == 0.9116
assert results.loc[1, '2.bb'] == 0.0186
assert results.loc[2, '300.aa'] == 0.0826
assert results.loc[2, '300.ab'] == 0.0316
assert results.loc[2, '300.bb'] == 0.8858
assert results.loc[3, '299.aa'] == 0.7988
assert results.loc[3, '299.ab'] == 0.1666
assert results.loc[3, '299.bb'] == 0.0346
assert results.loc[4, '150.aa'] == 0.0773
assert results.loc[4, '150.ab'] == 0.8683
assert results.loc[4, '150.bb'] == 0.0544
pos_values = results['pos'].unique()
assert len(pos_values) == 5
assert results.loc[0, 'pos'] == 18058
assert results.loc[1, 'pos'] == 18139
assert results.loc[2, 'pos'] == 18211
assert results.loc[3, 'pos'] == 18294
assert results.loc[4, 'pos'] == 18389
