def _context():
gwas = _gwas()
model = _prediction_model()
s = SampleData.dataframe_from_covariance(SampleData.sample_covariance_s_1())
covariance = MatrixManager.MatrixManager(s, D)
c = Utilities._build_context(model, covariance, gwas)
return c
def test_from_data(self):
s = SampleData.dataframe_from_covariance(
SampleData.sample_covariance_s_1())
m = MatrixManager.MatrixManager(s)
snps, cov = m.get("A")
self.assertEqual(snps, cov_data.SNPS_A)
numpy.testing.assert_array_almost_equal(cov, cov_data.COV_A)
snps, cov = m.get("B")
self.assertEqual(snps, cov_data.SNPS_B)
numpy.testing.assert_array_almost_equal(cov, cov_data.COV_B)
snps, cov = m.get("C")
self.assertEqual(snps, cov_data.SNPS_C)
numpy.testing.assert_array_almost_equal(cov, cov_data.COV_C)
snps, cov = m.get("C", ['rs100', 'rs101', 'rs102'])
self.assertEqual(snps, cov_data.SNPS_C)
numpy.testing.assert_array_almost_equal(cov, cov_data.COV_C)
with self.assertRaises(Exceptions.InvalidArguments) as ctx:
snps, cov = m.get("C", ["rs100", "rs12718973"])
self.assertTrue("whitelist" in ctx.exception.message)