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_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_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 setUp(self,
data_dir='example01',
bgen_names='chr{:d}impv1.bgen',
bgenix_path='bgenix',
user_pass_line=None):
super(TestRestApiGenotype, self).setUp()
# Load data
genoq = GenoQuery(get_repository_path(data_dir),
bgen_names=bgen_names,
bgenix_path=bgenix_path)
# Configure
app.app.config['testing'] = True
app.app.config['auth'] = None
app.app.config['genoquery'] = genoq
if user_pass_line is not None:
f = tempfile.NamedTemporaryFile(delete=False)
f.close()
with open(f.name, 'w') as fi:
fi.write(user_pass_line)
ph = PasswordHasher(f.name, method='pbkdf2:sha256')
app.app.config['auth'] = ph.setup_http_basic_auth()
self.app = app.app.test_client()
def setup_app(app, ph):
# Add GenoQuery object
genoq = GenoQuery(**config.get_genoquery_parameters())
app.config.update({'genoquery': genoq})
# Add Pheno2SQL object
p2sql = Pheno2SQL(**config.get_pheno2sql_parameters())
app.config.update({'pheno2sql': p2sql})
# Add auth object
auth = ph.setup_http_basic_auth()
app.config.update({'auth': auth})
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
from ukbrest import config
from ukbrest.common.utils.misc import update_parameters_from_args, parameter_empty
logger = config.logger
parser = config.get_argparse_arguments()
args = parser.parse_args()
# GenoQuery
genoq_parameters = config.get_genoquery_parameters()
genoq_parameters = update_parameters_from_args(genoq_parameters, args)
if parameter_empty(genoq_parameters, 'genotype_path'):
logger.warning('--genotype-path missing')
genoq = GenoQuery(**genoq_parameters)
app.config.update({'genoquery': genoq})
# Pheno2SQL
pheno2sql_parameters = config.get_pheno2sql_parameters()
pheno2sql_parameters = update_parameters_from_args(pheno2sql_parameters,
args)
if parameter_empty(pheno2sql_parameters, 'db_uri'):
parser.error('--db-uri missing')
p2sql = Pheno2SQL(**pheno2sql_parameters)
app.config.update({'pheno2sql': p2sql})
ph = PasswordHasher(args.users_file, method='pbkdf2:sha256')
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