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