cobramod.parsing.bigg
=====================

.. py:module:: cobramod.parsing.bigg

.. autoapi-nested-parse::

   Data parsing for BiGG

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

   - Metabolites: Normally, simple names.
   - Reactions: Mostly abbreviations.
   - Genes: It is included in the Reactions. Names and gene-reaction-rule is also
   acquired

   They change identifiers depending on the model given. BiGG have multiple models



Attributes
----------

.. autoapisummary::

   cobramod.parsing.bigg.debug_log


Functions
---------

.. autoapisummary::

   cobramod.parsing.bigg.find_url
   cobramod.parsing.bigg.build_reference
   cobramod.parsing.bigg.parse_reaction_attributes
   cobramod.parsing.bigg.parse_metabolite_attributes
   cobramod.parsing.bigg.parse_genes


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

.. py:data:: debug_log

.. py:function:: find_url(model_id, query)

   Tries to find a valid URL for the API of BIGG. It will return a
   :class:`requests.Response` if URL is valid.
   object

   :param model_id: Name for the specific BIGG model identifier.
   :type model_id: str
   :param identifier: Identifier for the item. Can be a reaction or
                      compound
   :type identifier: str

   :returns:

             A valid request Response followed by the database
                 Version.
   :rtype: (Response,str)

   :raises HTTPError: If identifier is not found in BIGG database.


.. py:function:: build_reference(json_data)

   Return a dictionary of cross-references, where the keys are the
   cross-references and values the their identifiers.


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

.. py:function:: parse_metabolite_attributes(data)

.. py:function:: parse_genes(data, rule)