cobramod.parsing.kegg
=====================

.. py:module:: cobramod.parsing.kegg

.. autoapi-nested-parse::

   Data parsing for KEGG

   This module handles the retrieval of data from KEGG into a local directory.
   The possible type of data that can be downloaded:

   - Metabolite: Identifiers that start with the letter C, e.g C00001
   - Reactions: Identifiers that start with the letter R, e.g R00001. The
   gene information for reactions is also included if the specie is specified
   - Module Pathways: Identifiers that start with the letter M, e.g M00001



Attributes
----------

.. autoapisummary::

   cobramod.parsing.kegg.debug_log
   cobramod.parsing.kegg.KO_LINK


Exceptions
----------

.. autoapisummary::

   cobramod.parsing.kegg.WrongParserError


Functions
---------

.. autoapisummary::

   cobramod.parsing.kegg.parse_metabolite_attributes
   cobramod.parsing.kegg.parse_reaction_attributes
   cobramod.parsing.kegg.data_from_string
   cobramod.parsing.kegg.build_references
   cobramod.parsing.kegg.ko_generator
   cobramod.parsing.kegg.parse_ko_to_genes
   cobramod.parsing.kegg.retrieve_kegg_genes
   cobramod.parsing.kegg.parse_genes
   cobramod.parsing.kegg.get_graph
   cobramod.parsing.kegg.parse_pathway_attributes


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

.. py:data:: debug_log

.. py:exception:: WrongParserError

   Bases: :py:obj:`Exception`


   Simple Error that should be raised if a method cannot handle the parsing.


.. py:data:: KO_LINK
   :value: 'http://rest.kegg.jp/link/ko/'


.. py:function:: parse_metabolite_attributes(data, entry)

.. py:function:: parse_reaction_attributes(data, entry, genome, gene_directory)

.. py:function:: data_from_string(raw)

   Formats most of the keys for KEGG data and returns a dictionary.


.. py:function:: build_references(data_dict)

   Return a dictionary, where the keys are the names of cross-references
   and keys their identifiers. If nothing is found, it will return None


.. py:function:: ko_generator(identifier)

   Returns a list with the corresponding KO-entries for given identifier.
   Otherwise it will raise a HTTPError


.. py:function:: parse_ko_to_genes(string, reaction, genome)

   Returns with a list with the corresponding genes for given genome. String
   is the raw text that include the gene information. If Abbreviation or no
   genome is present then, an empty list is returned.


.. py:function:: retrieve_kegg_genes(directory, identifier)

   Stores the genes for given reaction in given directory. Function will call
   a HTTPError if nothing is found.


.. py:function:: parse_genes(directory, identifier, genome)

   From given KEGG dictionary returns a dictionary with the key
   "genes" which include a dictionary with the identifier and name of the
   gene; and the key "rule" for the COBRApy representation of the
   gene-reaction rule


.. py:function:: get_graph(kegg_dict)

   Returns dictionary with sequences for a graph, where the key the prior
   reaction is and the value, its successor; and a set with all participant
   reaction (vertex)


.. py:function:: parse_pathway_attributes(data, entry)