cobramod.parsing.biocyc
=======================

.. py:module:: cobramod.parsing.biocyc

.. autoapi-nested-parse::

   Data parsing for Biocyc

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

   - Metabolites: Normally have an abbreviation or short name.
   - Reactions: Can have the words "RXN" in the identifier. Enzymes can sometimes
   be used instead. The gene information for the reactions is included if found.



Attributes
----------

.. autoapisummary::

   cobramod.parsing.biocyc.debug_log


Functions
---------

.. autoapisummary::

   cobramod.parsing.biocyc.build_cross_references_xml
   cobramod.parsing.biocyc.reaction_str_from_xml
   cobramod.parsing.biocyc.get_direction_from_xml
   cobramod.parsing.biocyc.parse_reaction_attributes
   cobramod.parsing.biocyc.parse_metabolite_attributes
   cobramod.parsing.biocyc.get_graph
   cobramod.parsing.biocyc.parse_pathway_attributes
   cobramod.parsing.biocyc.retrieve_gene_information
   cobramod.parsing.biocyc.parse_genes


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

.. py:data:: debug_log

.. py:function:: build_cross_references_xml(root)

   Returns a dictionary with the corresponding cross-references and their
   identifiers.


.. py:function:: reaction_str_from_xml(root)

.. py:function:: get_direction_from_xml(root)

   Returns the direction of the chemical reaction


.. py:function:: parse_reaction_attributes(root, entry, gene_directory)

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

.. py:function:: get_graph(root)

   Return a directed graph from given XML Element. A key represent the
   parent reaction and the value is the child. A parent can have multiple
   children as tuples. End-reactions have a NoneType as child.

   :param root: An XML element, which represent a XML file with the
                information of a pathway.
   :type root: Element

   :returns: Directed graph from root.
   :rtype: Dict

   :raises WrongParserError: If given root does not represent a pathway.


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

.. py:function:: retrieve_gene_information(directory, identifier, database)

   Retrieve the gene information for given reaction in a specific database
   :param directory: Directory to store and retrieve local data.
   :type directory: Path
   :param identifier: original identifier
   :type identifier: str
   :param database: Name of the database. Some options: "META", "ARA".
                    Full list in: "https://biocyc.org/biocyc-pgdb-list.shtml"
   :type database: str

   :raises HTTPError: If given reaction does not have gene information available


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

   Returns a dictionary with the corresponding genes and gene-reaction rules.
   This function will try to read a file for given identifier. If nothing is
   found, the dictionary will have empty entries.