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

.. py:module:: microbetag.helpers

.. autoapi-nested-parse::

   Handlers classes allowing the different steps



Attributes
----------

.. autoapisummary::

   microbetag.helpers.emojis


Classes
-------

.. autoapisummary::

   microbetag.helpers.Emojis
   microbetag.helpers.PathwayComplementarity
   microbetag.helpers.MappingPaths
   microbetag.helpers.Faprotax
   microbetag.helpers.NetworkHandler
   microbetag.helpers.AbdTableHandler
   microbetag.helpers.BinsHandler
   microbetag.helpers.SeedComplementarityHandler


Functions
---------

.. autoapisummary::

   microbetag.helpers.manta_input_net
   microbetag.helpers.otf_seqid_ncbi_gtdb_map


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

.. py:class:: Emojis

.. py:data:: emojis

.. py:class:: PathwayComplementarity(config: microbetag.config.Config)

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

   :param config: An instance of the :class:`.config.Config` class.

   .. note::

      From the :class:`.config.Config` class, the following attributes are being used:
          - `base_dir`
          - `ouput_dir`
          - `prev_path_compl`
          - `kofam_database`
          - `complement_max_length`
          - `ko_merged_file`
          - `pc_percentage`


   .. 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:: output_dirs()

      Paths to output folders and files



.. py:class:: MappingPaths

   Sets paths to mapping files


.. py:class:: Faprotax(config)

   Paths to FAPROTAX `collapse_table.py` script and database


.. py:class:: NetworkHandler(config)

   Set network-related configuration variables based on whether a network is already available or not.
   Check whether all the sequence identifiers present in the network as nodes, are also among those
   of the abundance table.


   .. py:method:: process_network(config)

      Process network edgelist and check bin consistency.



.. py:class:: AbdTableHandler(config)

   Handles processing and validation of the abundance table related variables.

   :param config: Instance of the :class:`Config` class


   .. 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)

   Handles bin/genomes/MAGs related variables in case of using microbetag with local/custom genomes.


.. py:class:: SeedComplementarityHandler(config)

   Handles variables related to building GENRES and the seed complementarity module.

   :param config: Instance of the :class:`Config` class


   .. py:method:: reconstrucion_paths(config)

      Set pathways for seeds related files and folders



   .. py:method:: seeds_paths(config)


.. py:function:: manta_input_net(config: microbetag.config.Config) -> bool

   Wrapper for building the intermediate network CYJSON file; input for manta


.. py:function:: otf_seqid_ncbi_gtdb_map(config: microbetag.config.Config) -> tuple[dict, dict, pandas.DataFrame]

   Builds a dataframe with sequence ids of nodes A and B found associated in the
   co-occurrence network followed by their corresponding NCBI Taxonomy ids and the
   representative GTDB genomes.

   :returns:     - pairs_of_interest: {("",""). ("","")}
                 - relative_genomes: {ncbi_id: [gc, gc, gc], ..}
                 - mspecies_map_df: A data frame with the sequence ids of the abundance data and
                     their mapped NCBI Taxonomy IDs and their corresponding GTDB representative genomes.
   :rtype: A tuple containing

   .. note:: Strictly for the on-the-fly version