:py:mod:`micom.workflows.db_media`
==================================

.. py:module:: micom.workflows.db_media

.. autoapi-nested-parse::

   Test growth media for a model database.



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


Functions
~~~~~~~~~

.. autoapisummary::

   micom.workflows.db_media._grow
   micom.workflows.db_media._try_complete
   micom.workflows.db_media.check_db_medium
   micom.workflows.db_media.complete_db_medium
   micom.workflows.db_media._annotate
   micom.workflows.db_media.db_annotations



.. py:function:: _grow(args)

   Get the maximum growth rate under a given medium.


.. py:function:: _try_complete(args)

   Try to complete the medium for a model.


.. py:function:: check_db_medium(model_db, medium, threads=1)

   Complete a growth medium for all models in a database.

   :param model_db: A pre-built model database. If ending in `.qza` must be a Qiime 2
                    artifact of type `MetabolicModels[JSON]`. Can also be a folder,
                    zip (must end in `.zip`) file or None if the taxonomy contains a
                    column `file`.
   :type model_db: str
   :param medium: A growth medium. Must have columns "reaction" and "flux" denoting
                  exchange reactions and their respective maximum flux. Can not be sample
                  specific.
   :type medium: pd.DataFrame
   :param threads: The number of parallel workers to use when building models. As a
                   rule of thumb you will need around 1GB of RAM for each thread.
   :type threads: int >=1

   :returns: Returns an annotated manifest file with a column `can_grow` that tells you
             whether the model can grow on the (fixed) medium, and a column `growth_rate`
             that gives the growth rate.
   :rtype: pd.DataFrame


.. py:function:: complete_db_medium(model_db, medium, growth=0.001, max_added_import=1, minimize_components=False, weights=None, threads=1, strict=list())

   Complete a growth medium for all models in a database.

   :param model_db: A pre-built model database. If ending in `.qza` must be a Qiime 2
                    artifact of type `MetabolicModels[JSON]`. Can also be a folder,
                    zip (must end in `.zip`) file or None if the taxonomy contains a
                    column `file`.
   :type model_db: str
   :param medium: A growth medium. Must have columns "reaction" and "flux" denoting
                  exchange reactions and their respective maximum flux. Can not be sample
                  specific.
   :type medium: pd.DataFrame
   :param growth: The minimum growth rate the model has to achieve with the (fixed) medium. If
                  a Series will have a minimum growth rate for each id/taxon in the model db.
   :type growth: positive float or pandas.Series
   :param max_added_import: Maximum import flux for each added additional import not included in the growth
                            medium. If positive will expand the medium with additional imports in order to
                            fulfill the growth objective.
   :type max_added_import: positive float
   :param minimize_components: Whether to minimize the number of components instead of the total
                               import flux. Might be more intuitive if set to True but may also be
                               slow to calculate.
   :type minimize_components: boolean
   :param weights: Will scale the fluxes by a weight factor. Can either be "mass" which will
                   scale by molecular mass, a single element which will scale by
                   the elemental content (for instance "C" to scale by carbon content).
                   If None every metabolite will receive the same weight.
                   Will be ignored if `minimize_components` is True.
   :type weights: str
   :param threads: The number of parallel workers to use when building models. As a
                   rule of thumb you will need around 1GB of RAM for each thread.
   :type threads: int >=1
   :param strict: Whether to match the imports in the predefined medium exactly. For reactions IDs
                  listed here will not allow additional import of the components in the provided
                  medium. For example, if your input medium has a flux of 10 mmol/(gDW*h) defined
                  and the requested growth rate can only be fulfilled by ramping this up that
                  would be allowed in non-strict mode but forbidden in strict mode. To match all
                  medium components to strict mode use `strict=medium.global_id`.
   :type strict: list

   :returns: Returns an annotated manifest file with a column `can_grow` that tells you
             whether the model can grow on the (fixed) medium, and a column `added` that
             gives the number of added imports apart from the ones in the medium.
   :rtype: tuple of (manifest, import fluxes)


.. py:function:: _annotate(f)

   Get annotation for a model.


.. py:function:: db_annotations(model_db, threads=1)

   Get metabolite annotations from a model DB.

   :param model_db: A pre-built model database. If ending in `.qza` must be a Qiime 2
                    artifact of type `MetabolicModels[JSON]`. Can also be a folder,
                    zip (must end in `.zip`) file or None if the taxonomy contains a
                    column `file`.
   :type model_db: str
   :param threads: The number of parallel workers to use when building models. As a
                   rule of thumb you will need around 1GB of RAM for each thread.
   :type threads: int >=1

   :returns: Annotations for all exchanged metabolites.
   :rtype: pd.DataFrame