How to use the anndata.read_hdf function in anndata

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github theislab / scanpy / scanpy / readwrite.py View on Github external
f'{avail_exts}'
        )
    else:
        ext = is_valid_filename(filename, return_ext=True)
    is_present = _check_datafile_present_and_download(
        filename,
        backup_url=backup_url,
    )
    if not is_present: logg.debug(f'... did not find original file {filename}')
    # read hdf5 files
    if ext in {'h5', 'h5ad'}:
        if sheet is None:
            return read_h5ad(filename, backed=backed)
        else:
            logg.debug(f'reading sheet {sheet} from file {filename}')
            return read_hdf(filename, sheet)
    # read other file types
    path_cache = settings.cachedir / _slugify(filename).replace('.' + ext, '.h5ad')  # type: Path
    if path_cache.suffix in {'.gz', '.bz2'}:
        path_cache = path_cache.with_suffix('')
    if cache and path_cache.is_file():
        logg.info(f'... reading from cache file {path_cache}')
        return read_h5ad(path_cache)

    if not is_present:
        raise FileNotFoundError(f'Did not find file {filename}.')
    logg.debug(f'reading {filename}')
    if not cache and not suppress_cache_warning:
        logg.hint(
            'This might be very slow. Consider passing `cache=True`, '
            'which enables much faster reading from a cache file.'
        )