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
anduniversal_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__
(self, \*args, \*\*kwargs)Call self as a function.
run
(self[, product, max_predictions, …])Run pathway prediction for a desired product.
-
run
(self, 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
The list of adapter reactions.
- Return type