gapfillinghelper

GapfillingHelper

A class of functions that assist modifying models:

gfhelper = GapfillingHelper(blacklist = [], auto_sink = ["cpd02701_c", "cpd11416_c0", "cpd15302_c"])

  • blacklist list: The collection of IDs for reactions that will not be examined during gapfilling.

  • auto_sink list: The collection of IDs for reactions that represent biomass growth.

test_reaction_additions_againt_limits()

Returns the collection of genes for all roles of all complexes from the template reaction:

filtered = gfhelper.test_reaction_additions_againt_limits(model,reactions,tests)

  • model cobra.core.model.Model: The COBRA model whose reactions will be tested.

  • reactions list: The collection of COBRA reactions in the model that will be tested.

  • tests list: The collection of dictionaries for the tests, with keys of "media", "default_uptake", "default_excretion", "target", & "maximize".

Returns filtered cobra.core.dictlist.DictList: The collection of tests that contained an objective maximum of 1 and greater than the test limit.

build_model_extended_for_gapfilling()

Extends a model with reactions and metabolites from collections of source models and possibly templates:

gapfilling_penalties = gfhelper.build_model_extended_for_gapfilling(extend_with_template = True, source_models = [], input_templates = [], model_penalty = 1, reaction_scores = {})

  • extend_with_template bool: specifies whether the gapfilling penalties will be extended with a template.

  • source_models & input_templates list: The collections of models and templates whose reactions and metabolites be extend the object model before its gapfilling.

  • model_penalty int: The gapfilling penalty for reaction flux, with an equal weighting in both directions.

  • reaction_scores dict: The gapfilling reaction scores (values) for each gene of each reaction (keys).

Returns gapfilling_penalties dict: The gapfilling penalties of the extended model.

convert_modelreaction() & convert_modelcompound()

Formats COBRA reactions and metabolites for ModelSEED operations, respectively:

cobra_rxn = gfhelper.convert_modelreaction(reaction, bigg=False)
cobra_met = gfhelper.convert_modelreaction(metabolite, bigg=False)

  • reaction cobra.core.reaction.Reaction: The COBRA reaction that will be reformatted.

  • metabolite cobra.core.metabolite.Metabolite: The COBRA metabolite that will be reformatted.

  • bigg bool: specifies whether the COBRA object originates from a BiGG model, which requires an additional reformulation.

Returns cobra_rxn cobra.core.reaction.Reaction: The reaction that is generated from the ModelSEED reaction. Returns cobra_met cobra.core.metabolite.Metabolite: The metabolite that is generated from the ModelSEED metabolite.

binary_check_gapfilling_solution()

Constructs binary variables for the direction of all model reactions, the sum of which are minimized and the resulting fluxes are returned:

flux_values = gfhelper.binary_check_gapfilling_solution(gapfilling_penalties,add_solution_exclusion_constraint)

  • gapfilling_penalties dict: The collection of gapfilling penalties (values) for each direction of all reaction IDs (keys).

  • add_solution_exclusion_constraint bool: specifies whether a binary exclusion constraint will be added based upon the primal flux values, which renders a gapfilled solution infeasible and thus permits the determination of a new solution.

Returns flux_values dict: The collection of all primal flux values (values) for each direction of all reaction IDs (keys).

create_minimal_reaction_objective()

Constructs an objective function that minimizes the flux of gapfilled reactions:

gene = gfhelper.create_minimal_reaction_objective(penalty_hash, default_penalty = 0)

  • penalty_hash dict: The collection of gapfilling penalties (values) for each direction of all reaction IDs (keys), which will be minimized through this function.

  • default_penalty str: The default gapfill penalty and is the default flux coefficient in the objective function for all reactions.

convert_cobra_compound_to_kbcompound()

Constructs a metadata dictionary of a COBRA Metabolite object that is returned and can be added to a KBase model:

cpd_data = gfhelper.convert_cobra_compound_to_kbcompound(cpd, kbmodel=None)

  • cpd cobra.core.metabolite.Metabolite: The COBRA Metabolite that will be converted into a KBase Metabolite.

  • kbmodel cobrakbase model: The KBase model that will be expanded with cpd metadata, where None specifies that the compound will not be added.

Returns cpd_data dict: The collection of cpd attributes in key-value pairs.

convert_cobra_reaction_to_kbreaction()

Constructs a metadata dictionary of a COBRA Reaction object that is returned and can be added to a KBase model:

rxn_data = gfhelper.convert_cobra_reaction_to_kbreaction(rxn, kbmodel, direction="=", add_to_model=True)

  • rxn cobra.core.metabolite.Metabolite: The COBRA Metabolite that will be converted into a KBase Reaction.

  • kbmodel cobrakbase model: The KBase model that contains rxn.

  • direction str: The “<”, “=”, or “>” direction of rxn.

  • add_to_model bool: specifies whether the reaction metadata will be added to the KBase model.

Returns rxn_data dict: The collection of rxn attributes in key-value pairs.

convert_objective_to_constraint()

Coverts an old objective function into a variable and constructs a new constraint that the new objective must equate the old object. The variable and constraint are added to the cobramodel in the extant object:

gfhelper.convert_objective_to_constraint(lower_bound, upper_bound)

  • lower_bound & upper_bound float: The bounds that will contrain the objective function variable.

compute_gapfilled_solution()

Returns the direction for all gapfilled reactions in a model:

directions = gfhelper.compute_gapfilled_solution(penalty_hash, flux_values = None)

  • penalty_hash dict: The collection of gapfilling penalties (values) for each direction of all reaction IDs (keys), which will be minimized through this function.

  • flux_values dict: The collection of all primal flux values (values) for each direction of all reaction IDs (keys), where None constructs flux_values from the from cobramodel in class object.

Returns directions dict: The collection of directions (values) for all reactions in a cobramodel that are stored in penalty_hash.

add_gapfilling_solution_to_kbase_model()

The gapfilled reactions of a solution are added to a model:

gfhelper.add_gapfilling_solution_to_kbase_model(newmodel, penalty_hash, media_ref)

  • newmodel cobrakbase Model: The model to which the gapfilled content will be added.

  • penalty_hash dict: The collection of gapfilling penalties (values) for each direction of all reaction IDs (keys), which will be minimized through this function.

  • media_ref str: The reference of the media that was used to gapfill the model.

compute_reaction_scores()

Returns the gapfilling reaction scores for all events, with possible weighting:

reaction_genes = gfhelper.compute_reaction_scores(weights=None)

  • weights dict: The collection of gapfill-weightings (values) for each event, via "description", "event_id", or "id" attributes of the event (keys). An argument of None specifies that all events will be equally weighted.

Returns reaction_genes dict: The collection of reaction scores (values) for each gene of all reactions over all ontological events in fbamodel.

replicate_model()

Returns a new model that contains a parameterized number of duplicate content of the cobramodel in the class object:

newmodel = gfhelper.replicate_model(count)

  • count int: The number of copies of the cobramodel that are added to the new model.

Returns newmodel cobra.core.model.Model: The duplicated COBRA model.

test_reaction_additions_againt_limits()

Returns a new model that contains a parameterized number of duplicate content of the cobramodel in the class object:

newmodel = gfhelper.replicate_model(reactions, directions, tests)

  • reactions dict: The “<” or “>” reaction directions (values) for all COBRA reactions that will be tested (keys).

  • tests list: The collection of tests that will be examined for the reactions in the cobrakbase model.

Returns filtered_tests dict: The collection of reaction directions and reaction objects in key-value pairs.