def test_gene_list_filter(self):
npr1, nexp1 = ManagePriors.filter_to_gene_list(self.priors_data,
self.expression_matrix,
self.gene_list)
self.assertListEqual(nexp1.index.tolist(), self.gene_list)
self.assertListEqual(npr1.index.tolist(), self.gene_list)
gene_list2 = self.gene_list + ["fake1", "fake2"]
npr2, nexp2 = ManagePriors.filter_to_gene_list(self.priors_data,
self.expression_matrix,
gene_list2)
self.assertListEqual(nexp2.index.tolist(), self.gene_list)
self.assertListEqual(npr2.index.tolist(), self.gene_list)
with self.assertRaises(ValueError):
nexp3 = self.expression_matrix.copy()
nexp3.index = list(range(nexp3.shape[0]))
npr3, nexp3 = ManagePriors.filter_to_gene_list(
self.priors_data, nexp3, self.gene_list)
with self.assertRaises(ValueError):
npr3 = self.priors_data.copy()
npr3.index = list(range(npr3.shape[0]))
npr3, nexp3 = ManagePriors.filter_to_gene_list(
npr3, self.expression_matrix, self.gene_list)
def test_shuffle_index(self):
idx = list(range(20))
idx1 = ManagePriors._make_shuffled_index(20, seed=42)
idx2 = ManagePriors._make_shuffled_index(20, seed=42)
idx3 = ManagePriors._make_shuffled_index(20, seed=43)
self.assertListEqual(idx1, idx2)
self.assertFalse(idx == idx1)
self.assertFalse(idx1 == idx3)
self.assertEqual(len(set(idx1).symmetric_difference(set(idx))), 0)
self.assertEqual(len(set(idx1).symmetric_difference(set(idx2))), 0)
self.assertEqual(len(set(idx1).symmetric_difference(set(idx3))), 0)
def test_gene_list_filter(self):
npr1 = ManagePriors.filter_priors_to_genes(self.priors_data, self.gene_list)
self.assertListEqual(npr1.index.tolist(), self.gene_list)
gene_list2 = self.gene_list + ["fake1", "fake2"]
npr2 = ManagePriors.filter_priors_to_genes(self.priors_data, gene_list2)
self.assertListEqual(npr2.index.tolist(), self.gene_list)
with self.assertRaises(ValueError):
npr3 = ManagePriors.filter_priors_to_genes(self.priors_data, [])
with self.assertRaises(ValueError):
npr3 = self.priors_data.copy()
npr3.index = list(range(npr3.shape[0]))
npr3 = ManagePriors.filter_priors_to_genes(npr3, self.gene_list)
def test_priors_tf_names(self):
npr1 = ManagePriors.filter_to_tf_names_list(self.priors_data, self.tf_names)
self.assertListEqual(npr1.columns.tolist(), self.tf_names)
self.assertListEqual(npr1.index.tolist(), self.priors_data.index.tolist())
npr2 = ManagePriors.filter_to_tf_names_list(self.priors_data, self.tf_names[:10])
self.assertListEqual(npr2.columns.tolist(), self.tf_names[:10])
self.assertListEqual(npr2.index.tolist(), self.priors_data.index.tolist())
npr3 = ManagePriors.filter_to_tf_names_list(self.priors_data, self.tf_names + ["fake1", "fake2"])
self.assertListEqual(npr3.columns.tolist(), self.tf_names)
self.assertListEqual(npr3.index.tolist(), self.priors_data.index.tolist())
with self.assertRaises(ValueError):
ManagePriors.filter_to_tf_names_list(self.priors_data, ["fake1", "fake2"])
def test_align_priors_2(self):
npr = self.priors_data
npr.index = list(range(npr.shape[0]))
with self.assertRaises(ValueError):
npr = ManagePriors.align_priors_to_expression(
npr, self.expression_matrix)
def test_add_noise_to_priors(self):
npr1 = ManagePriors.add_prior_noise(self.priors_data,
1,
random_seed=50)
self.assertEqual(npr1.max().max(), 1)
self.assertEqual((npr1 != 0).sum().sum(), npr1.size)
def test_add_noise_to_no_priors(self):
priors_data = pd.DataFrame(0,
index=self.priors_data.index,
columns=self.priors_data.columns)
npr1 = ManagePriors.add_prior_noise(priors_data, 0.1, random_seed=50)
self.assertEqual((priors_data != 0).sum().sum(), 0)
self.assertEqual((npr1 != 0).sum().sum(), int(npr1.size * 0.1))
def test_align_priors_1(self):
npr = self.priors_data.iloc[list(range(10)), :]
npr = ManagePriors.align_priors_to_expression(npr,
self.data.gene_names)
self.assertEqual(len(npr.index), len(self.data.gene_names))
self.assertListEqual(npr.columns.tolist(),
self.priors_data.columns.tolist())
self.assertListEqual(npr.index.tolist(), self.data.gene_names.tolist())
def test_cv_downsample(self):
npr1, ngs1 = ManagePriors.cross_validate_gold_standard(self.priors_data, self.gold_standard, None, 0.5, 42)
self.assertEqual(npr1.shape, ngs1.shape)
self.assertListEqual(npr1.index.tolist(), ngs1.index.tolist())
self.assertListEqual(npr1.columns.tolist(), ngs1.columns.tolist())
self.assertEqual((npr1 != 0).sum().sum(), (ngs1 != 0).sum().sum() * 0.5)
self.assertEqual((self.gold_standard != 0).sum().sum(), (ngs1 != 0).sum().sum())
pdt.assert_frame_equal(self.gold_standard, ngs1)
def test_validation_passthrough(self):
ngs = self.gold_standard
ngs.index = ["A"] * ngs.shape[0]
ngs.columns = ["B"] * ngs.shape[1]
npr = self.priors_data
npr.index = ["C"] * npr.shape[0]
npr.columns = ["D"] * npr.shape[1]
npr1, ngs1 = ManagePriors.validate_priors_gold_standard(npr, ngs)
pdt.assert_frame_equal(ngs, ngs1)
pdt.assert_frame_equal(npr, npr1)
def test_cv_genes(self):
npr1, ngs1 = ManagePriors.cross_validate_gold_standard(
self.priors_data, self.gold_standard, 0, 0.5, 42)
self.assertEqual(npr1.shape, ngs1.shape)
self.assertEqual(len(npr1.index.intersection(ngs1.index)), 0)
pdt.assert_index_equal(npr1.columns, self.priors_data.columns)
pdt.assert_index_equal(ngs1.columns, self.gold_standard.columns)
npr2, ngs2 = ManagePriors.cross_validate_gold_standard(
self.priors_data, self.gold_standard, 0, 0.5, 43)
npr3, ngs3 = ManagePriors.cross_validate_gold_standard(
self.priors_data, self.gold_standard, 0, 0.5, 42)
pdt.assert_frame_equal(npr1, npr3)
pdt.assert_frame_equal(ngs1, ngs3)
with self.assertRaises(AssertionError):
pdt.assert_frame_equal(npr1, npr2)
with self.assertRaises(AssertionError):
pdt.assert_frame_equal(ngs1, ngs2)
def test_cv_tfs(self):
npr1, ngs1 = ManagePriors.cross_validate_gold_standard(
self.priors_data, self.gold_standard, 1, 0.5, 42)
self.assertEqual(npr1.shape, ngs1.shape)
self.assertEqual(len(npr1.columns.intersection(ngs1.columns)), 0)
def test_cv_genes(self):
npr1, ngs1 = ManagePriors.cross_validate_gold_standard(
self.priors_data, self.gold_standard, 0, 0.5, 42)
self.assertEqual(npr1.shape, ngs1.shape)
self.assertEqual(len(npr1.index.intersection(ngs1.index)), 0)
def test_shuffle_priors_tf(self):
npr3 = ManagePriors.shuffle_priors(self.priors_data, 1, 42)
pdt.assert_series_equal(self.priors_data.sum(axis=1), npr3.sum(axis=1))
pdt.assert_index_equal(npr3.index, self.priors_data.index)
pdt.assert_index_equal(npr3.columns, self.priors_data.columns)
def test_shuffle_priors_gene(self):
npr2 = ManagePriors.shuffle_priors(self.priors_data, 0, 42)
pdt.assert_series_equal(self.priors_data.sum(axis=0), npr2.sum(axis=0))
pdt.assert_index_equal(npr2.index, self.priors_data.index)
pdt.assert_index_equal(npr2.columns, self.priors_data.columns)
def test_shuffle_priors_none(self):
npr1 = ManagePriors.shuffle_priors(self.priors_data, None, 42)
pdt.assert_frame_equal(npr1, self.priors_data)
