def test_hdf5(self):
file, data = test_prebuilt.counts_yeast_single_cell_chr01(filetype='hdf5')
self.worker.set_expression_file(hdf5=file)
self.worker.read_expression()
npt.assert_array_almost_equal(data.values, self.worker.data.expression_data)
def test_mtx(self):
(file1, file2, file3), data = test_prebuilt.counts_yeast_single_cell_chr01(filetype='mtx')
self.worker.set_expression_file(mtx=file1, mtx_feature=file2, mtx_barcode=file3)
self.worker.read_expression()
npt.assert_array_almost_equal(data.values, self.worker.data.expression_data.A)
def test_tsv(self):
file, data = test_prebuilt.counts_yeast_single_cell_chr01(filetype='tsv')
data.to_csv(file, sep="\t")
self.worker.set_expression_file(tsv=file)
self.worker.read_expression()
npt.assert_array_almost_equal(data.values, self.worker.data.expression_data)
def test_10x_ranger3(self):
(file1, file2, file3), data = test_prebuilt.counts_yeast_single_cell_chr01(filetype='mtx', gzip=True)
with tempfile.TemporaryDirectory() as txdir:
shutil.copy(file1, os.path.join(txdir, "matrix.mtx.gz"))
shutil.copy(file2, os.path.join(txdir, "features.tsv.gz"))
shutil.copy(file3, os.path.join(txdir, "barcodes.tsv.gz"))
self.worker.set_expression_file(tenx_path=txdir)
self.worker.read_expression()
npt.assert_array_almost_equal(data.values, self.worker.data.expression_data.A)
