class TestSnpIdCoefDao(unittest.TestCase): #--------------------------------------------- # Constants #--------------------------------------------- #--------------------------------------------- # Setup Methods #--------------------------------------------- def setUp(self): '''Use a localhost UCSC copy.''' self.engine = create_engine(DEFAULT_URL) self.idcoef_dao = DEFAULT_SNP_DB_DAOS().idcoef_dao # Base.metadata.create_all(self.engine) def tearDown(self): '''Drop the database.''' pass #--------------------------------------------- # Test Methods #--------------------------------------------- def test_num_records(self): '''Test getting the total # of SNP records.''' assert_equal(self.idcoef_dao.num_records(), 1415 * 1416 / 2, 'Wrong row count from SNP table') def test_delta(self): '''Test retrieving condensed identity coefficient for a pair of samples.''' lam, delta = self.idcoef_dao.id_coefs(168042, 163352) assert_almost_equal(lam, 0.341689, decimal=5, err_msg='Wrong SNP lambda coefficient loading from db') assert_almost_equal(delta, np.array([6.89670924e-05, 0.0016811301, 0.00197529634, 0.0418526094, 0.00258931545, 0.0338666878, 0.00123981348, 0.0908498468, 0.825876333]), decimal=5, err_msg='Wrong SNP Delta loading from db')
class TestSnpIdCoefDao(unittest.TestCase): #--------------------------------------------- # Constants #--------------------------------------------- #--------------------------------------------- # Setup Methods #--------------------------------------------- def setUp(self): '''Use a localhost UCSC copy.''' self.engine = create_engine(DEFAULT_URL) self.idcoef_dao = DEFAULT_SNP_DB_DAOS().idcoef_dao # Base.metadata.create_all(self.engine) def tearDown(self): '''Drop the database.''' pass #--------------------------------------------- # Test Methods #--------------------------------------------- def test_num_records(self): '''Test getting the total # of SNP records.''' assert_equal(self.idcoef_dao.num_records(), 1415 * 1416 / 2, 'Wrong row count from SNP table') def test_delta(self): '''Test retrieving condensed identity coefficient for a pair of samples.''' lam, delta = self.idcoef_dao.id_coefs(168042, 163352) assert_almost_equal( lam, 0.341689, decimal=5, err_msg='Wrong SNP lambda coefficient loading from db') assert_almost_equal(delta, np.array([ 6.89670924e-05, 0.0016811301, 0.00197529634, 0.0418526094, 0.00258931545, 0.0338666878, 0.00123981348, 0.0908498468, 0.825876333 ]), decimal=5, err_msg='Wrong SNP Delta loading from db')
def setUp(self): '''Use a localhost UCSC copy.''' self.engine = create_engine(DEFAULT_URL) self.idcoef_dao = DEFAULT_SNP_DB_DAOS().idcoef_dao