scanpy.read

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

Read file and return AnnData object.

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

Parameters:
filename : 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 : {False, True, ‘r’, ‘r+’}, optional (default: False)

Load AnnData in backed mode instead of fully loading it into memory (memory mode). Only applies to .h5ad files. True and ‘r’ are equivalent. If you want to modify backed attributes of the AnnData object, you need to choose ‘r+’.

sheet : str, optional (default: None)

Name of sheet/table in hdf5 or Excel file.

cache : bool, optional (default: False)

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

ext : str, optional (default: None)

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

delimiter : str, optional (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, optional (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, optional (default: None)

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

Returns:

adata

Return type:

AnnData