cameo.strain_design.pathway_prediction package

Submodules

cameo.strain_design.pathway_prediction.pathway_predictor module

class cameo.strain_design.pathway_prediction.pathway_predictor.PathwayPredictor(model, universal_model=None, mapping=None, compartment_regexp=None)[source]

Bases: cameo.core.strain_design.StrainDesignMethod

Pathway predictions from a universal set of reaction.

Parameters:
  • model (cobra.Model) – The model that represents the host organism.
  • universal_model (cobra.Model, optional) – The model that represents the universal set of reactions. A default model will be used if omitted.
  • mapping (dict, optional) – A dictionary that contains a mapping between metabolite identifiers in model and universal_model
  • compartment_regexp (str, optional) – A regular expression that matches host metabolites’ compartments that should be connected to the universal reaction model. If not provided, the compartment containing most metabolites will be chosen.
model

The provided model + universal_model + adapter reactions

Type:cobra.Model

Examples

Determine production pathways for propane-1,3-diol (MNXM2861 in the metanetx namespace)

>>> from cameo.api import hosts
>>> pathway_predictor = PathwayPredictor(hosts.ecoli.iJO1366)
>>> pathway_predictor.run(product=pathway_predictor.model.metabolites.MNXM2861)

Methods

__call__(*args, **kwargs) Call self as a function.
run([product, max_predictions, …]) Run pathway prediction for a desired product.
run(product=None, max_predictions=inf, min_production=0.1, timeout=None, callback=None, silent=False, allow_native_exchanges=False)[source]

Run pathway prediction for a desired product.

Parameters:
  • product (Metabolite, str) – Metabolite or id or name of metabolite to find production pathways for.
  • max_predictions (int, optional) – The maximum number of predictions to compute.
  • min_production (float) – The minimum acceptable production flux to product.
  • timeout (int) – The time limit [seconds] per attempted prediction.
  • callback (function) – A function that takes a successfully predicted pathway.
  • silent (bool) – If True will print the pathways and max flux values.
  • allow_native_exchanges (bool) – If True, exchange reactions for native metabolites will be allowed.
Returns:

The predicted pathways.
Return type:

PathwayPredictions

cameo.strain_design.pathway_prediction.util module

cameo.strain_design.pathway_prediction.util.create_adapter_reactions(original_metabolites, universal_model, mapping, compartment_regexp)[source]

Create adapter reactions that connect host and universal model.

Parameters:
  • original_metabolites (list) – List of host metabolites.
  • universal_model (cobra.Model) – The universal model.
  • mapping (dict) – A mapping between between host and universal model metabolite IDs.
  • compartment_regexp (regex) – A compiled regex that matches metabolites that should be connected to the universal model.
Returns:

reactions – The list of adapter reactions.
Return type:

list
cameo.strain_design.pathway_prediction.util.display_pathway(pathway, i)[source]

Module contents