segmentation
============

.. py:module:: segmentation

.. autoapi-nested-parse::

   Classes that interact with the outputs of different protein segmentations



Submodules
----------

.. toctree::
   :maxdepth: 1

   /autoapi/segmentation/chainsaw/index
   /autoapi/segmentation/geostas/index
   /autoapi/segmentation/merizo/index








Package Contents
----------------

.. py:exception:: ParsingError

   Bases: :py:obj:`Exception`


   Raised when an issue was encountered during parsing the inputs. Will
   contain as ``__cause__`` the original exception that triggered it.


.. py:class:: SegmentationParser(*paths: list[pathlib.Path | str])

   The base class for all segmentation parsers.


   .. py:attribute:: paths
      :value: ()



   .. py:method:: parse() -> collections.abc.Iterator[Tuple[str, int, str]]
      :abstractmethod:


      The return value is a collection of items of the form::

          ("<method name>", <number of domains>, "<chopping>")

      They could be collected into a list or yield-ed. The
      :func:`write_segmentations` function only expects that this method
      returns an iterable object.



.. py:function:: write_segmentations(seg_objects: list[SegmentationParser], output_file: pathlib.Path | str)

   Invoke the given segmentation parsers and collect their output in a TSV.