cameo.core package¶

cameo.core.manipulation module¶

Manage manipulations such as swapping reaction cofactors, over-express or down-regulate genes and reactions.

cameo.core.manipulation.increase_flux(reaction, ref_value, value)[source]

lb 0 ub |--------------------------- ' ---------------------------|

<- - -|———-‘
‘———-|- - - ->
Parameters: reaction (cobra.Reaction) – The reaction to over-express. ref_value (float) – The flux value to come from. value (float) – The flux value to achieve.
cameo.core.manipulation.decrease_flux(reaction, ref_value, value)[source]

lb 0 ub |--------------------------- ' ---------------------------|

|- - >———-‘
‘———-<- - - -|
Parameters: reaction (cobra.Reaction) – The reaction to down_regulate. ref_value (float) – The flux value to come from. value (float) – The flux value to achieve.
cameo.core.manipulation.reverse_flux(reaction, ref_value, value)[source]

Forces a reaction to have a minimum flux level in the opposite direction of a reference state.

lb 0 ub |--------------------------- ' ---------------------------|

<———-‘- - - - - - - ->
Parameters: reaction (cobra.Reaction) – The reaction that will be inverted. ref_value (float) – The flux value to come from. value (float) – The flux value to achieve.
cameo.core.manipulation.swap_cofactors(reaction, model, swap_pairs, inplace=True)[source]

Swaps the cofactors of a reaction. For speed, it can be done inplace which just changes the coefficients. If not done inplace, it will create a new Reaction, add it to the model, and knockout the original reaction.

Parameters: reaction (cobra.Reaction) – The reaction to swap. model (cameo.cobra.Model) – A constraint-based model. swap_pairs (tuple) – A tuple of (cofactors, equivalent_cofactors) inplace (bool) – If replace is done inplace, it changes the coefficients in the matrix. Otherwise, it creates a new reaction with the other cofactors and adds it to the model. A reaction with swapped cofactors (the same if inplace). Reaction

cameo.core.model_dual module¶

cameo.core.model_dual.convert_to_dual(model)[source]
cameo.core.model_dual.to_dual_model(model, solver_interface=None)[source]
class cameo.core.model_dual.ModelDual(*args, **kwargs)[source]

Bases: cobra.core.model.Model

A cobra.Model that also contains the dual variables and constraints, allowing primal and dual problems to be combined.

Dual variables corresponding to stoichiometric constraints are prefixed by lambda Dual variables corresponding to flux bounds are prefixed by mu Other constraints are not supported at the moment!

Dual constraints will be set according to the original primal objective. The objective can be changed subsequently to optimize an outer problem.

Attributes

Methods

objective

Get or set the solver objective

Before introduction of the optlang based problems, this function returned the objective reactions as a list. With optlang, the objective is not limited a simple linear summation of individual reaction fluxes, making that return value ambiguous. Henceforth, use cobra.util.solver.linear_reaction_coefficients to get a dictionary of reactions with their linear coefficients (empty if there are none)

The set value can be dictionary (reactions as keys, linear coefficients as values), string (reaction identifier), int (reaction index), Reaction or problem.Objective or sympy expression directly interpreted as objectives.

When using a HistoryManager context, this attribute can be set temporarily, reversed when the exiting the context.

dual_objective
primal_objective()[source]

cameo.core.pathway module¶

This module implements a pathway data structure that can be added to a model for example.

class cameo.core.pathway.Pathway(reactions, *args, **kwargs)[source]

Bases: object

Representation of a pathway (a set of reactions)

reactions

list o Reaction – The list of reactions in the pathway.

Attributes

Methods

data_frame
classmethod from_file(file_path, sep='\t')[source]

The equation is defined by: coefficient * substrate_name#substrate_id + … <=> coefficient * product_name#product_id

Parameters: file_path (str) – The path to the file containing the pathway sep (str) – The separator between elements in the file (default: ” “) Pathway
to_file(file_path, sep='\t')[source]

Writes the pathway to a file.

Parameters: file_path (str) – The path to the file where the pathway will be written sep (str) – The separator between elements in the file (default: ” “)
plug_model(model)[source]

Plugs the pathway to a model.

Metabolites are matched in the model by id. For metabolites with no ID in the model, an exchange reaction is added to the model

Parameters: model (cobra.Model) – The model to plug in the pathway

cameo.core.result module¶

class cameo.core.result.MetaInformation(*args, **kwargs)[source]

Bases: object

Attributes

system_info
responsible
timestamp

doc string

human_readable_timestamp
class cameo.core.result.Result(*args, **kwargs)[source]

Bases: object

Attributes

Methods

meta_information
data_frame
plot(grid=None, width=None, height=None, title=None, *args, **kwargs)[source]

cameo.core.strain_design module¶

Core implementation of strain design. It contains core structures. Targets (and subclasses) are identified by strain design methods.

class cameo.core.strain_design.StrainDesignMethod(*args, **kwargs)[source]

Bases: object

Methods

run(*args, **kwargs)[source]
class cameo.core.strain_design.StrainDesign(targets)[source]

Bases: object

A StrainDesign is a collection of targets in a COBRA model. The targets, identified by a StrainDesignMethod, map elements in the model that need to be modified to achieve the objective of the design method.

Methods

apply(model)[source]
to_gnomic()[source]
class cameo.core.strain_design.StrainDesignMethodResult(designs, *args, **kwargs)[source]

Attributes

Methods

data_frame
display_on_map(index, map_name)[source]
plot(grid=None, width=None, height=None, title=None, *args, **kwargs)[source]

cameo.core.target module¶

class cameo.core.target.ReactionCofactorSwapTarget(id, swap_pairs, *args, **kwargs)[source]

Bases: cameo.core.target.Target

Swap cofactors of a given reaction.

Attributes

Methods

apply(model)[source]

Applies the modification on the target, depending on the target type.

Subclass()

swap_str
to_gnomic()[source]

If gnomic is available, return a Gnomic representation of the Target.

class cameo.core.target.ReactionKnockinTarget(id, value, *args, **kwargs)[source]

Bases: cameo.core.target.KnockinTarget

Methods

apply(model)[source]

Applies the modification on the target, depending on the target type.

Subclass()

to_gnomic()[source]

If gnomic is available, return a Gnomic representation of the Target.

class cameo.core.target.GeneModulationTarget(id, value, reference_value, *args, **kwargs)[source]

Bases: cameo.core.target.FluxModulationTarget

Attributes

Methods

get_model_target(model)[source]
class cameo.core.target.GeneKnockoutTarget(id, *args, **kwargs)[source]

Gene Knockout Target. Knockout a gene present in a COBRA model.

Attributes

Methods

apply(model)[source]

Applies a change to the flux. If the fold change is higher than 0 it increases the flux. If the target flux is zero it applies a knockout. If the fold change is lower than 0, then it decreases the flux.

Parameters: model (cobra.Model) – A model.
to_gnomic()[source]

If gnomic is available, return a Gnomic representation of the Target.

class cameo.core.target.ReactionModulationTarget(id, value, reference_value)[source]

Bases: cameo.core.target.FluxModulationTarget

Attributes

Methods

get_model_target(model)[source]
class cameo.core.target.ReactionKnockoutTarget(id)[source]

Reaction Knockout Target. Knockout a reaction present in a COBRA model.

Attributes

Methods

apply(model)[source]

Applies a change to the flux. If the fold change is higher than 0 it increases the flux. If the target flux is zero it applies a knockout. If the fold change is lower than 0, then it decreases the flux.

Parameters: model (cobra.Model) – A model.

cameo.core.utils module¶

cameo.core.utils.get_reaction_for(model, value, add=True)[source]

Get or create a reaction for a metabolite or a reaction.

If value is a Metabolite or a Metabolite id, return any already existing demand or exchange reaction. If add is true, add a demand reaction if it does not already exist.

Parameters: model (cobra.Model) – The model to for which to get / create a reaction value (str, Reaction or Metabolite) – A reaction identifier, a Reaction or a Metabolite for which an exchange reaction is to be created. add (bool) – Adds a demand reaction for a metabolite if a metabolite is found for value Reaction KeyError – If value does not match any Reaction or Metabolite
cameo.core.utils.medium(model)[source]

Current medium for this model.

cameo.core.utils.load_medium(model, medium_def, copy=False, delimiter='\t')[source]

Loads a medium into the model. If copy is true it will return a copy of the model. Otherwise it applies the medium to itself. Supported formats TODO

Parameters: model (cobra.Model) – The model to load medium for medium_def (str, pandas.DataFrame, dict.) – The medium to load copy (boolean, optional) – If True copies the model, otherwise the changes will happen inplace. delimiter (str) – Only if loading the medium from a file. If copy=True, returns a copy of the model. cobra.Model

Module contents¶

This package implements the basic data structures (models, reactions etc.) used in cameo.