skbio.io.registry.read

skbio.io.registry.read(self, file, format=None, into=None, verify=True, **kwargs)[source]

Read file as format into an object.

State: Stable as of 0.4.0.

Parameters:
  • file (openable (filepath, URL, filehandle, etc.)) – The file to read. Something that is understood by skbio.io.open.
  • format (str, optional) – The format of the file if known. If None, the format will be inferred from the file.
  • into (type or None, optional) – The object which will be returned. If None, a generator will be returned.
  • verify (bool, optional) – When True, will double check the format if provided.
  • kwargs (dict, optional) – Keyword arguments will be passed to their respective handlers (skbio.io.open and the reader for format). newline cannot be provided.
Returns:

An instance of into if into is not None else generator
Return type:

object or 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.