medusa.core

Package Contents

class medusa.core.Ensemble(list_of_models=[], identifier=None, name=None)

Bases:cobra.core.object.Object

Ensemble of metabolic models

Parameters:
  • identifier (string) – The identifier to associate with the ensemble as a string.
  • list_of_models (list of cobra.core.model.Model) – Either a list of existing Model objects in which case a new Model object is instantiated and an ensemble is constructed using the list of Models, or None/empty list, in which case an ensemble is created with empty attributes.
  • name (string) – Human-readable name for the ensemble
base_model

A cobra.core.Model that contains all variable and invariable components of an ensemble.

Type:Model
members

A DictList where the key is the member identifier and the value is a medusa.core.member.Member object

Type:DictList
features

A DictList where the key is the feature identifier and the value is a medusa.core.feature.Feature object

Type:DictList
_populate_features_base(self, list_of_models)
_populate_members(self, list_of_models)
set_state(self, member)

Set the state of the base model to represent a single member.

Sets all features to the state for the provided member. Only reaction states are currently implemented (e.g. GPRs as features will not work)

Parameters:member (str or medusa.Member) – The Member.id, or the Member object itself, to set the state of the Ensemble.base_model to represent.
to_pickle(self, filename)

Save an ensemble as a pickled object. Pickling is currently the only supported method for saving and loading ensembles.

Parameters:filename (String) – location to save the pickle.
extract_member(self, member)

Extract an individual member as a cobrapy model (cobra.Model), removing any components associated with features that are inactive in member.

Provided as a more convenient option than medusa.Member.to_model(), but is the exact same.

Parameters:member (str or medusa.Member) – The Member.id, or the Member object itself, to be represented in the cobrapy model output.
Returns:model – The extracted member as a cobrapy model.
Return type:cobra.Model
class medusa.core.Feature(identifier=None, name=None, ensemble=None, base_component=None, component_attribute=None, states=None)

Bases:cobra.core.object.Object

Feature describing a network component that varies across an ensemble.

Parameters:
  • identifier (string) – The identifier to associate with the feature. Convention is to append the component_attribute to the base_component’s id.
  • ensemble (medusa.core.ensemble.Ensemble object) – The ensemble that the feature is associated with.
  • base_component (cobra.core.reaction.Reaction) – Reference to the Reaction object that the feature describes.
  • component_attribute (string) – string indicating the attribute of base_component that the feature describes the modification of (e.g. “lb”, “ub”)
  • states (dictionary of string:component_attribute value) – dictionary of model ids mapping to the value of the Feature’s component_attribute (value type depends on component_attribute type, e.g. float for “lb”, string for “_gene_reaction_rule”)
get_model_state(self, member_id)

Get the state of the feature for a particular member

class medusa.core.Member(ensemble=None, identifier=None, name=None, states=None)

Bases:cobra.core.object.Object

Object representing an individual member (i.e. model) in an ensemble

Parameters:
  • identifier (string) – The identifier to associate with the member.
  • ensemble (medusa.core.ensemble.Ensemble object) – The ensemble that the member belongs to.
  • states (dictionary of medusa.core.feature.Feature:component_attribute value) – dictionary of Features mapping to the value of the Feature’s component_attribute (value type depends on component_attribute type, e.g. float for “lb”, string for “_gene_reaction_rule”) for the member.
to_model(self)

Generate a cobra.Model object with the exact state of this member.

The resulting cobra.Model does not contain any Metabolites, Genes, or Reactions that were inactive in the member.

Returns:model – The extracted member as a cobrapy model.
Return type:cobra.Model
_set_id_with_model(self, value)