def setUp(self):
self.entrezs = np.array([1,2])
self.labels = np.array([1,1,1,0,0,0])
self.expr_data = np.array([[1,0,1,1,0,1],
[0,1,0,1,0,1]])
self.expression = Expression(self.expr_data, self.entrezs, self.labels, binarize=False)
class TestExpression(unittest.TestCase):
def setUp(self):
self.entrezs = np.array([1,2])
self.labels = np.array([1,1,1,0,0,0])
self.expr_data = np.array([[1,0,1,1,0,1],
[0,1,0,1,0,1]])
self.expression = Expression(self.expr_data, self.entrezs, self.labels, binarize=False)
def tearDown(self):
pass
def test_init(self):
np.testing.assert_array_equal(self.expression.gene_sample, self.expr_data)
np.testing.assert_array_equal(self.expression.sample_gene, self.expr_data.T)
def test_num_genes(self):
self.assertEqual(self.expression.num_genes(), len(self.entrezs))
def test_num_samples(self):
self.assertEqual(self.expression.num_samples(), len(self.labels))
self.assertEqual(self.expression.num_samples(1), np.sum(self.labels == 1))
self.assertEqual(self.expression.num_samples(0), np.sum(self.labels == 0))
def test_subset(self):
eids = [1]
g, e, l = self.expression.subset(eids)
np.testing.assert_array_equal(g, np.array([self.expr_data[0]]))
np.testing.assert_array_equal(e, eids)
np.testing.assert_array_equal(l, self.labels)
def test_subset_clone(self):
expression = Expression(*self.expression.subset(list(self.entrezs)), binarize=False)
self.assertEqual(expression.num_samples(), len(self.labels))
self.assertEqual(expression.num_genes(), len(self.entrezs))
np.testing.assert_array_equal(expression.gene_sample, self.expr_data)
def test_binarize(self):
alpha = 0.25
expression = Expression(self.expr_data, self.entrezs, self.labels, binarize=True,
alpha=alpha)
self.assertEqual(expression.gene_sample.sum(), int(expression.gene_sample.size * alpha))
def test_index_of_gene(self):
self.assertEqual(self.expression.index_of_gene(2), 1)
def test_subset_clone(self):
expression = Expression(*self.expression.subset(list(self.entrezs)), binarize=False)
self.assertEqual(expression.num_samples(), len(self.labels))
self.assertEqual(expression.num_genes(), len(self.entrezs))
np.testing.assert_array_equal(expression.gene_sample, self.expr_data)
