Modules
=======

Funannotate2 consists of several modules that handle different aspects of the annotation process.

funannotate2.clean
----------------

.. automodule:: funannotate2.clean
   :members:
   :undoc-members:
   :show-inheritance:

The clean module provides functions for cleaning and preparing genome assemblies for annotation.

funannotate2.predict
-----------------

.. automodule:: funannotate2.predict
   :members:
   :undoc-members:
   :show-inheritance:

The predict module provides functions for predicting genes in genome assemblies.

funannotate2.annotate
------------------

.. automodule:: funannotate2.annotate
   :members:
   :undoc-members:
   :show-inheritance:

The annotate module provides functions for functionally annotating predicted genes.


funannotate2.search
----------------

.. automodule:: funannotate2.search
   :members:
   :undoc-members:
   :show-inheritance:

The search module provides functions for searching sequences against various databases.

funannotate2.utilities
------------------

.. automodule:: funannotate2.utilities
   :members:
   :undoc-members:
   :show-inheritance:

The utilities module provides utility functions used by other modules.

funannotate2.log
-------------

.. automodule:: funannotate2.log
   :members:
   :undoc-members:
   :show-inheritance:

The log module provides logging functions used by other modules.