def test_sum_anndatas(self):
adata_spliced = utils.import_matrix_as_anndata(
self.spliced_matrix_path, self.spliced_barcodes_path,
self.spliced_genes_path)
adata_unspliced = utils.import_matrix_as_anndata(
self.unspliced_matrix_path, self.unspliced_barcodes_path,
self.unspliced_genes_path)
adata = utils.sum_anndatas(adata_spliced, adata_unspliced)
self.assertEqual(2.0, adata.X[5, 15])
def test_overlay_anndatas(self):
adata_spliced = utils.import_matrix_as_anndata(
self.spliced_matrix_path, self.spliced_barcodes_path,
self.spliced_genes_path)
adata_unspliced = utils.import_matrix_as_anndata(
self.unspliced_matrix_path, self.unspliced_barcodes_path,
self.unspliced_genes_path)
adata = utils.overlay_anndatas(adata_spliced, adata_unspliced)
self.assertEqual({'spliced', 'unspliced'}, set(adata.layers.keys()))
def test_import_matrix_as_anndata_name(self):
adata = utils.import_matrix_as_anndata(
self.matrix_path, self.barcodes_path, self.genes_path, name='test'
)
self.assertIsInstance(adata, anndata.AnnData)
self.assertEqual(set(), set(adata.var))
self.assertEqual(set(), set(adata.obs))
self.assertEqual('test_id', adata.var.index.name)
self.assertEqual('barcode', adata.obs.index.name)
def test_import_matrix_as_anndata(self):
adata = utils.import_matrix_as_anndata(self.matrix_path,
self.barcodes_path,
self.genes_path)
self.assertIsInstance(adata, anndata.AnnData)
self.assertEqual((29, 17), adata.shape)
self.assertEqual(set(), set(adata.var))
self.assertEqual(set(), set(adata.obs))
self.assertEqual('gene_id', adata.var.index.name)
self.assertEqual('barcode', adata.obs.index.name)
self.assertEqual(1, adata.X[9, 0])
self.assertEqual(1, adata.X[15, 0])
def test_import_matrix_as_anndata_with_t2g(self):
adata = utils.import_matrix_as_anndata(self.matrix_path,
self.barcodes_path,
self.genes_path,
t2g_path=self.t2g_path)
self.assertIsInstance(adata, anndata.AnnData)
self.assertEqual(set(), set(adata.obs))
self.assertEqual('gene_id', adata.var.index.name)
self.assertEqual('barcode', adata.obs.index.name)
self.assertEqual([
'Clk1', 'Serpinb10', 'Olfr421-ps1', 'Olfr335-ps', 'Olfr1001-ps1',
'Olfr1010', 'Olfr1021-ps1', 'Olfr1038-ps', 'Olfr1077-ps1',
'Olfr1083-ps', 'Olfr1117-ps1', 'Olfr1165-ps', 'Olfr475-ps1',
'Olfr1267-ps1', 'Olfr1268-ps1', 'Olfr1273-ps', 'Olfr1300-ps1'
], list(adata.var.gene_name.values))
def test_import_matrix_as_anndata_duplicated(self):
adata = utils.import_matrix_as_anndata(
self.matrix_duplicated_path,
self.barcodes_path,
self.genes_duplicated_path,
)
self.assertIsInstance(adata, anndata.AnnData)
self.assertEqual(set(), set(adata.obs))
self.assertEqual('gene_id', adata.var.index.name)
self.assertEqual('barcode', adata.obs.index.name)
self.assertEqual((29, 16), adata.shape)
self.assertNotIn('ENSMUSG00000092572.7', adata.var.index)
self.assertEqual(
5, adata.X[15,
adata.var.index.get_loc('ENSMUSG00000026034.17')])