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_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