1.4 Converting Gene or Reaction Knockouts into Metabolite Knockouts
=======================================================================

.. code:: ipython3

    from marsi.cobra.strain_design.post_processing import replace_strain_design_results

.. code:: ipython3

    from cameo import models
    from cameo.strain_design import OptGene
    from cameo.util import TimeMachine
    from pandas import DataFrame

Design a D-lactate producing strain
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In this example we are going to create strain designs using OptGene.

+-----------+-----------+--------------+---------------+
| Model     | Medium    | Aerobicity   | Target        |
+===========+===========+==============+===============+
| iJO1366   | Glucose   | Anaerobic    | lac\_\_D\_e   |
+-----------+-----------+--------------+---------------+

.. code:: ipython3

    model = models.bigg.iJO1366

.. code:: ipython3

    model.reactions.EX_o2_e.lower_bound = 0

We search for reactions, because they can be directly translated into
metabolite targets

.. code:: ipython3

    optgene = OptGene(model, manipulation_type="reactions", essential_reactions=["ATPM"])

.. code:: ipython3

    results = optgene.run(target="EX_lac__D_e", 
                          biomass="BIOMASS_Ec_iJO1366_core_53p95M",
                          substrate="EX_glc__D_e",
                          max_knockouts=15,
                          max_evaluations=15000)

.. code:: ipython3

    df = results.data_frame

.. code:: ipython3

    df

.. code:: ipython3

    replacements = replace_strain_design_results(model, results, results._objective_function, 
                                                 results._simulation_method, results._simulation_kwargs)

.. code:: ipython3

    replacements.style