skbio.io.registry.IORegistry.read#

IORegistry.read(file, format=None, into=None, verify=True, **kwargs)[source]#

Read a file as certain format into an object.

Parameters:
fileopenable (filepath, URL, filehandle, etc.)

The file to read. Something that is understood by skbio.io.open().

formatstr, optional

The format of the file if known. If None, the format will be inferred from the file.

intotype or None, optional

The object which will be returned. If None, a generator will be returned.

verifybool, optional

When True, will double check the format if provided.

kwargsdict, optional

Keyword arguments will be passed to their respective handlers (skbio.io.open() and the reader for format). newline cannot be provided.

Returns:
object or generator

An instance of into if into is not None else generator

Raises:
ValueError

Raised when format and into are both None.

TypeError

If newline is provided in kwargs.

UnrecognizedFormatError

Raised when a reader could not be found for a given format or the format could not be guessed.

FormatIdentificationWarning

Raised when verify is True and the sniffer of a format did not agree that file is a member of format

ArgumentOverrideWarning

Raised when verify is True and a user-supplied argument is overriding the suggestion provided by the sniffer of format.