def test_get_data_loader(self):
self.assertIsInstance(get_data_loader("matrix.mtx"), MtxLoader)
self.assertIsInstance(get_data_loader("lib.cell.count"), CountLoader)
loader = get_data_loader("DATA_MATRIX_LOG_TPM.txt")
self.assertIsInstance(loader, Loader)
self.assertIsInstance(get_data_loader("data.xls"), ExcelLoader)
self.assertIsInstance(get_data_loader("data.loom"), LoomLoader)
def test_n_genes_n_cells(self):
file_name = os.path.join(os.path.dirname(__file__),
"data/10x/hg19/matrix.mtx")
loader = get_data_loader(file_name)
self.assertEqual(loader.n_genes, loader.n_rows)
self.assertEqual(loader.n_cells, loader.n_cols)
file_name = os.path.join(os.path.dirname(__file__),
"DATA_MATRIX_LOG_TPM.txt")
loader = get_data_loader(file_name)
self.assertEqual(loader.n_genes, loader.n_rows)
self.assertEqual(loader.n_cells, loader.n_cols)
def set_current_path(self, path):
if samepath(self._current_path, path):
return
model = self.recent_model
index = -1
pathitem = None
for i in range(model.rowCount()):
item = model.item(i)
data = item.data(Qt.UserRole) if item is not None else None
if isinstance(data, RecentPath) and samepath(path, data.abspath):
index, pathitem = i, data
break
rpaths = []
if pathitem is None:
assert index == -1
pathitem = RecentPath.create(path, rpaths)
if index != -1:
item = model.takeRow(index)
else:
item = RecentPath_asqstandarditem(pathitem)
model.insertRow(0, item)
self._current_path = path
self.recent_combo.setCurrentIndex(0)
self._data_loader = get_data_loader(path)
self._update_summary()
self.setup_gui()
self._invalidate()
def test_get_data_loader_compressed_file(self):
loader = get_data_loader("lib.cell.count.gz")
self.assertIsInstance(loader, CountLoader)
def test_get_data_loader_pickle(self):
self.assertIsInstance(get_data_loader("data.pkl"), PickleLoader)
self.assertIsInstance(get_data_loader("data.pickle"), PickleLoader)