:mod:`memote.support.annotation`
================================

.. py:module:: memote.support.annotation

.. autoapi-nested-parse::

   Supporting functions for annotation checks performed on the model object.

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


Functions
~~~~~~~~~

.. autoapisummary::

   memote.support.annotation.find_components_without_annotation
   memote.support.annotation.generate_component_annotation_overview
   memote.support.annotation.generate_component_annotation_miriam_match
   memote.support.annotation.generate_component_id_namespace_overview


.. data:: LOGGER
   

   

.. data:: GENE_PRODUCT_ANNOTATIONS
   

   

.. data:: REACTION_ANNOTATIONS
   

   

.. data:: METABOLITE_ANNOTATIONS
   

   

.. function:: find_components_without_annotation(model, components)

   Find model components with empty annotation attributes.


   :Parameters:

       **model** : cobra.Model
           A cobrapy metabolic model.

       **components** : {"metabolites", "reactions", "genes"}
           A string denoting `cobra.Model` components.

   :Returns:

       list
           The components without any annotation.













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.. function:: generate_component_annotation_overview(elements, db)

   Tabulate which MIRIAM databases the component's annotation match.


   :Parameters:

       **elements** : list
           Elements of a model, either metabolites, reactions, or genes.

       **db** : str
           One of the MIRIAM database identifiers.

   :Returns:

       list
           The components that are not annotated with the specified MIRIAM
           database.













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.. function:: generate_component_annotation_miriam_match(elements, component, db)

   Tabulate which MIRIAM databases the element's annotation match.

   If the relevant MIRIAM identifier is not in an element's annotation it is
   ignored.

   :Parameters:

       **elements** : list
           Elements of a model, either metabolites or reactions.

       **component** : {"metabolites", "reactions"}
           A string denoting a type of ``cobra.Model`` component.

       **db** : str
           One of the MIRIAM database identifiers.

   :Returns:

       list
           The components whose annotation does not match the pattern for the
           MIRIAM database.













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.. function:: generate_component_id_namespace_overview(model, components)

   Tabulate which MIRIAM databases the component's identifier matches.


   :Parameters:

       **model** : cobra.Model
           A cobrapy metabolic model.

       **components** : {"metabolites", "reactions", "genes"}
           A string denoting `cobra.Model` components.

   :Returns:

       pandas.DataFrame
           The index of the table is given by the component identifiers. Each
           column corresponds to one MIRIAM database and a Boolean entry
           determines whether the annotation matches.













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