microbetag.helpers
==================

.. py:module:: microbetag.helpers

.. autoapi-nested-parse::

   Handlers classes allowing the different steps







Module Contents
---------------

.. py:class:: PathwayComplementarity(config)

   Sets variables regarding pathway complementarity tasks based on user's config (.yml) file


   .. py:method:: setup_kegg_annotations()

      Sets up KEGG annotations and directories.



   .. py:method:: get_kofam_db_path()

      Returns the KOfam database path.



   .. py:method:: handle_missing_kofam_db()

      Handles the case when the KOfam database path is missing.



   .. py:method:: initialize(conf)

      Main function to initialize pathway complementarity settings.



   .. py:method:: setup_ko_merged()

      Sets up the KO merged file.



   .. py:method:: output_dirs(config)

      Paths to output folders and files



.. py:class:: MappingPaths(config)

   Sets paths to mapping files


.. py:class:: Faprotax(config)

.. py:class:: NetworkHandler(config)

   .. py:method:: process_network(config)

      Process network edgelist and check bin consistency.



.. py:class:: AbdTableHandler(config)

   .. py:method:: load_abundance_table(config)

      Reads and validates the abundance table.



   .. py:method:: load_metadata_file(config)

      Load metadata file if provided



.. py:class:: BinsHandler(config)

.. py:class:: SeedComplementarityHandler(config)

   .. py:method:: seeds_paths(config)

      Set pathways for seeds related files and folders



.. py:function:: manta_input_net(config)

   Build intermediate network file as input for manta


.. py:class:: Emojis

.. py:function:: local_seed_url()

   Builds KEGG urls for seed complements.
   Function to be used out of the pipeline