class TestFileIdCoefDao(unittest.TestCase):
#---------------------------------------------
# Constants
#---------------------------------------------
#---------------------------------------------
# Setup Methods
#---------------------------------------------
def setUp(self):
'''Use a localhost UCSC copy.'''
self.idcoef_dao = IdCoefDao(tu.abs_path('pedigree/example.id'))
self.kinship_dao = KinshipDao(tu.abs_path('pedigree/example.kinship'))
#---------------------------------------------
# Test Methods
#---------------------------------------------
def test_num_records(self):
'''Test getting the total # of SNP records.'''
assert_equal(self.idcoef_dao.num_records(), 3**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 file')
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 file')
def test_kinship(self):
'''Test retrieving kinship coefficients for a pair of samples.'''
assert_equal(self.kinship_dao.num_records(), 3**2,
'Wrong row count from SNP table')
_, delta = self.idcoef_dao.id_coefs(168042, 163352)
f = self.kinship_dao.kinship(168042, 163352)
assert_almost_equal(
f,
_kinship(delta),
decimal=5,
err_msg=
'Kinship coefficient does not match value derived from identity coefficients'
)
class TestFileIdCoefDao(unittest.TestCase):
#---------------------------------------------
# Constants
#---------------------------------------------
#---------------------------------------------
# Setup Methods
#---------------------------------------------
def setUp(self):
'''Use a localhost UCSC copy.'''
self.idcoef_dao = IdCoefDao(tu.abs_path('pedigree/example.id'))
self.kinship_dao = KinshipDao(tu.abs_path('pedigree/example.kinship'))
#---------------------------------------------
# Test Methods
#---------------------------------------------
def test_num_records(self):
'''Test getting the total # of SNP records.'''
assert_equal(self.idcoef_dao.num_records(), 3 ** 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 file')
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 file')
def test_kinship(self):
'''Test retrieving kinship coefficients for a pair of samples.'''
assert_equal(self.kinship_dao.num_records(), 3 ** 2, 'Wrong row count from SNP table')
_, delta = self.idcoef_dao.id_coefs(168042, 163352)
f = self.kinship_dao.kinship(168042, 163352)
assert_almost_equal(f, _kinship(delta),
decimal=5, err_msg='Kinship coefficient does not match value derived from identity coefficients')
def setUp(self):
'''Use a localhost UCSC copy.'''
self.idcoef_dao = IdCoefDao(tu.abs_path('pedigree/example.id'))
self.kinship_dao = KinshipDao(tu.abs_path('pedigree/example.kinship'))
def setUp(self):
'''Use a localhost UCSC copy.'''
self.idcoef_dao = IdCoefDao(tu.abs_path('pedigree/example.id'))
self.kinship_dao = KinshipDao(tu.abs_path('pedigree/example.kinship'))