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_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_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