scanpy.read

scanpy.read(filename, backed=None, *, sheet=None, ext=None, delimiter=None, first_column_names=False, backup_url=None, cache=False, cache_compression=_empty, **kwargs)

Read file and return AnnData object.

To speed up reading, consider passing cache=True, which creates an hdf5 cache file.

Parameters:

filename PathLike[str] | str

If the filename has no file extension, it is interpreted as a key for generating a filename via sc.settings.writedir / (filename + sc.settings.file_format_data). This is the same behavior as in sc.read(filename, ...).

backed Optional[Literal['r', 'r+']] (default: None)

If 'r', load AnnData in backed mode instead of fully loading it into memory (memory mode). If you want to modify backed attributes of the AnnData object, you need to choose 'r+'.

sheet str | None (default: None)

Name of sheet/table in hdf5 or Excel file.

ext str | None (default: None)

Extension that indicates the file type. If None, uses extension of filename.

delimiter str | None (default: None)

Delimiter that separates data within text file. If None, will split at arbitrary number of white spaces, which is different from enforcing splitting at any single white space ' '.

first_column_names bool (default: False)

Assume the first column stores row names. This is only necessary if these are not strings: strings in the first column are automatically assumed to be row names.

backup_url str | None (default: None)

Retrieve the file from an URL if not present on disk.

cache bool (default: False)

If False, read from source, if True, read from fast ‘h5ad’ cache.

cache_compression Union[Literal['gzip', 'lzf'], None, Empty] (default: _empty)

See the h5py Filter pipeline. (Default: settings.cache_compression)

kwargs

Parameters passed to read_loom().

Return type:

AnnData

Returns:

An AnnData object