scvelo.read

scvelo.read(filename, backed=None, sheet=None, ext=None, delimiter=None, first_column_names=False, backup_url=None, cache=False, cache_compression=<Empty.token: 0>, **kwargs)

Read file and return AnnData object.

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

Parameters

filename : Path, 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 : _Literalgenericalias[r, r+], 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

Name of sheet/table in hdf5 or Excel file.

ext : str, None

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

delimiter : str, 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

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

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

cache : bool

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

cache_compression : _Literalgenericalias[gzip, lzf], None, Empty

See the h5py dataset_compression. (Default: settings.cache_compression)

kwargs

Parameters passed to read_loom().

Return type

AnnData

Returns

An AnnData object