skbio.io.registry.Format.reader

Format.reader(cls, override=False)

Decorate a function to act as the reader for a class in this format.

The function should take an argument which will be an implementation of either io.TextIOBase or io.BufferedReader depending on if the format is text or binary, respectively. Any kwargs given by the user which are not handled by skbio.io.util.open() will be passed into the function. Any kwarg with a default of FileSentinel will transform user input for that parameter into a filehandle or None if not provided.

Parameters:

clstype or None

The class which the function will be registered to handle. If None, it is assumed that the function will produce a generator.

overridebool, optional

If True, any existing readers for cls in this format will be overriden.

Raises:

DuplicateRegistrationError

When override is False and a reader is already registered to cls for this format.

Examples

>>> from skbio.io.registry import Format, io_registry
>>> from skbio.io.registry import Read, Write
>>> myformat = Format('myformat')
>>> io_registry.add_format(myformat)
>>> # If developing a new format for skbio, use the create_format()
>>> # factory instead of the above.
>>> class MyObject:
...     read = Read()
...     write = Write()
...     def __init__(self, content):
...         self.content = content
...
>>> @myformat.reader(MyObject)
... def myformat_reader(fh):
...     return MyObject(fh.readlines()[1:])
...
>>> MyObject.read(["myformat2\n", "some content here!\n"],
...               format='myformat').content
['some content here!\n']
>>> # Cleanup
>>> io_registry.remove_format('myformat')