def test_double_index(subset_func, subset_func2):
    adata = gen_adata((10, 10))
    obs_subset = subset_func(adata.obs_names)
    var_subset = subset_func2(adata.var_names)
    v1 = adata[obs_subset, var_subset]
    v2 = adata[obs_subset, :][:, var_subset]

    assert np.all(asarray(v1.X) == asarray(v2.X))
    assert np.all(v1.obs == v2.obs)
    assert np.all(v1.var == v2.var)
def ProcessCommandLineArgs(parser, args):
  # TODO(ariblue): Delete this flag entirely at some future data, when the
  # existence of such a flag has been long forgotten.
  if args.output_file:
    parser.error('This flag is deprecated. Please use --output-dir instead.')

  try:
    os.makedirs(args.output_dir)
  except OSError:
    # Do nothing if the output directory already exists. Existing files will
    # get overwritten.
    pass

  args.output_dir = os.path.expanduser(args.output_dir)