Source code for cobra.flux_analysis.essentiality

from warnings import warn
    from cobra.flux_analysis.moma import moma
    warn("moma does not appear to be functional on your system")
from cobra.manipulation import initialize_growth_medium

[docs]def assess_medium_component_essentiality(cobra_model, the_components=None, the_medium=None, medium_compartment='e', solver='glpk', the_condition=None, method='fba'): """Determines which components in an in silico medium are essential for growth in the context of the remaining components. cobra_model: A Model object. the_components: None or a list of external boundary reactions that will be sequentially disabled. the_medium: Is None, a string, or a dictionary. If a string then the initialize_growth_medium function expects that the_model has an attribute dictionary called media_compositions, which is a dictionary of dictionaries for various medium compositions. Where a medium composition is a dictionary of external boundary reaction ids for the medium components and the external boundary fluxes for each medium component. medium_compartment: the compartment in which the boundary reactions supplying the medium components exist NOTE: that these fluxes must be negative because the convention is backwards means something is feed into the system. solver: 'glpk', 'gurobi', or 'cplex' returns: essentiality_dict: A dictionary providing the maximum growth rate accessible when the respective component is removed from the medium. """ if method.lower() == 'moma': wt_model = cobra_model.copy() cobra_model = cobra_model.copy() if isinstance(the_medium, str): try: the_medium = cobra_model.media_compositions[the_medium] except: raise Exception( the_medium + " is not in cobra_model.media_compositions") if the_medium is not None: initialize_growth_medium(cobra_model, the_medium, medium_compartment) if the_components is None: the_components = the_medium.keys() if not the_components: raise Exception("You need to specify the_components or the_medium") essentiality_dict = {} for the_component in the_components: the_reaction = cobra_model.reactions.get_by_id(the_component) original_lower_bound = float(the_reaction.lower_bound) the_reaction.lower_bound = 0. if method.lower() == 'fba': cobra_model.optimize(solver=solver) objective_value = cobra_model.solution.f elif method.lower() == 'moma': objective_value = moma(wt_model, cobra_model, solver=solver)[ 'objective_value'] essentiality_dict[the_component] = objective_value the_reaction.lower_bound = original_lower_bound return(essentiality_dict)