cobamp.wrappers package

Submodules

cobamp.wrappers.external_wrappers module

class cobamp.wrappers.external_wrappers.AbstractObjectReader(model)

Bases: object

An abstract class for reading metabolic model objects from external frameworks, and extracting the data needed for pathway analysis methods. Also deals with name conversions.

convert_constraint_ids(tup, yield_constraint)

convert_gprs_to_list(rx, apply_fx)

decode_k_shortest_solution(solarg)

g2rx(expression, and_fx=<built-in function min>, or_fx=<built-in function max>, as_vector=False, apply_fx=None)

get_gene_protein_reaction_rule(id)

get_irreversibilities(as_index)

Returns a vector representing irreversible reactions, either as a vector of booleans (each value is a flux, ordered in the same way as reaction identifiers) or as a vector of reaction indexes.

Parameters

as_dict: A boolean value that controls whether the result is a vector of indexes

get_model_bounds(as_dict, separate_list)

Returns the lower and upper bounds for all fluxes in the model. This either comes in the form of an ordered list with tuples of size 2 (lb,ub) or a dictionary with the same tuples mapped by strings with reaction identifiers.

Parameters

as_dict: A boolean value that controls whether the result is a dictionary mapping str to tuple of size 2 separate: A boolean value that controls whether the result is two numpy.array(), one for lb and the other

to ub

get_model_genes()

Returns the identifiers for the genes contained in the model

get_model_gprs(apply_fx=None)

Returns the model gene-protein-reaction rules associated with each reaction

get_reaction_and_metabolite_ids()

Returns two ordered iterables containing the metabolite and reaction ids respectively.

get_rx_instances()

Returns the reaction instances contained in the model. Varies depending on the framework.

get_stoichiometric_matrix()

Returns a 2D numpy array with the stoichiometric matrix whose metabolite and reaction indexes match the names defined in the class variables r_ids and m_ids

get_working_gene_names()

metabolite_id_to_index(id)

Returns the numerical index of a metabolite when given a string representing its identifier.

Parameters

id: A metabolite identifier as a string

reaction_id_to_index(id)

Returns the numerical index of a reaction when given a string representing its identifier.

Parameters

id: A reaction identifier as a string

to_cobamp_cbm(solver=None)

class cobamp.wrappers.external_wrappers.COBRAModelObjectReader(model)

Bases: cobamp.wrappers.external_wrappers.AbstractObjectReader

convert_gprs_to_list(rx, apply_fx)

get_irreversibilities(as_index)

Returns a vector representing irreversible reactions, either as a vector of booleans (each value is a flux, ordered in the same way as reaction identifiers) or as a vector of reaction indexes.

Parameters

as_dict: A boolean value that controls whether the result is a vector of indexes

get_model_bounds(as_dict=False, separate_list=False)

Returns the lower and upper bounds for all fluxes in the model. This either comes in the form of an ordered list with tuples of size 2 (lb,ub) or a dictionary with the same tuples mapped by strings with reaction identifiers.

Parameters

as_dict: A boolean value that controls whether the result is a dictionary mapping str to tuple of size 2 separate: A boolean value that controls whether the result is two numpy.array(), one for lb and the other

to ub

get_model_genes()

Returns the identifiers for the genes contained in the model

get_model_gprs(apply_fx=None, token_to_gene_ratio=20)

Returns the model gene-protein-reaction rules associated with each reaction

get_reaction_and_metabolite_ids()

Returns two ordered iterables containing the metabolite and reaction ids respectively.

get_rx_instances()

Returns the reaction instances contained in the model. Varies depending on the framework.

get_stoichiometric_matrix()

Returns a 2D numpy array with the stoichiometric matrix whose metabolite and reaction indexes match the names defined in the class variables r_ids and m_ids

class cobamp.wrappers.external_wrappers.CobampModelObjectReader(model)

Bases: cobamp.wrappers.external_wrappers.AbstractObjectReader

get_irreversibilities(as_index)

Returns a vector representing irreversible reactions, either as a vector of booleans (each value is a flux, ordered in the same way as reaction identifiers) or as a vector of reaction indexes.

Parameters

as_dict: A boolean value that controls whether the result is a vector of indexes

get_model_bounds(as_dict, separate_list=False)

Returns the lower and upper bounds for all fluxes in the model. This either comes in the form of an ordered list with tuples of size 2 (lb,ub) or a dictionary with the same tuples mapped by strings with reaction identifiers.

Parameters

as_dict: A boolean value that controls whether the result is a dictionary mapping str to tuple of size 2 separate: A boolean value that controls whether the result is two numpy.array(), one for lb and the other

to ub

get_reaction_and_metabolite_ids()

Returns two ordered iterables containing the metabolite and reaction ids respectively.

get_rx_instances()

Returns the reaction instances contained in the model. Varies depending on the framework.

get_stoichiometric_matrix()

Returns a 2D numpy array with the stoichiometric matrix whose metabolite and reaction indexes match the names defined in the class variables r_ids and m_ids

class cobamp.wrappers.external_wrappers.FramedModelObjectReader(model)

Bases: cobamp.wrappers.external_wrappers.AbstractObjectReader

convert_gprs_to_list(rx)

get_irreversibilities(as_index)

Returns a vector representing irreversible reactions, either as a vector of booleans (each value is a flux, ordered in the same way as reaction identifiers) or as a vector of reaction indexes.

Parameters

as_dict: A boolean value that controls whether the result is a vector of indexes

get_model_bounds(as_dict=False, separate_list=False)

Returns the lower and upper bounds for all fluxes in the model. This either comes in the form of an ordered list with tuples of size 2 (lb,ub) or a dictionary with the same tuples mapped by strings with reaction identifiers.

Parameters

as_dict: A boolean value that controls whether the result is a dictionary mapping str to tuple of size 2 separate: A boolean value that controls whether the result is two numpy.array(), one for lb and the other

to ub

get_reaction_and_metabolite_ids()

Returns two ordered iterables containing the metabolite and reaction ids respectively.

get_rx_instances()

Returns the reaction instances contained in the model. Varies depending on the framework.

get_stoichiometric_matrix()

Returns a 2D numpy array with the stoichiometric matrix whose metabolite and reaction indexes match the names defined in the class variables r_ids and m_ids

class cobamp.wrappers.external_wrappers.MatFormatReader(model)

Bases: cobamp.wrappers.external_wrappers.AbstractObjectReader

convert_gprs_to_list(rx, apply_fx)

get_irreversibilities(as_index)

Returns a vector representing irreversible reactions, either as a vector of booleans (each value is a flux, ordered in the same way as reaction identifiers) or as a vector of reaction indexes.

Parameters

as_dict: A boolean value that controls whether the result is a vector of indexes

get_model_bounds(as_dict=False, separate_list=False)

Returns the lower and upper bounds for all fluxes in the model. This either comes in the form of an ordered list with tuples of size 2 (lb,ub) or a dictionary with the same tuples mapped by strings with reaction identifiers.

Parameters

as_dict: A boolean value that controls whether the result is a dictionary mapping str to tuple of size 2 separate: A boolean value that controls whether the result is two numpy.array(), one for lb and the other

to ub

get_model_genes()

Returns the identifiers for the genes contained in the model

get_model_gprs(apply_fx=None)

Returns the model gene-protein-reaction rules associated with each reaction

get_reaction_and_metabolite_ids()

Returns two ordered iterables containing the metabolite and reaction ids respectively.

get_rx_instances()

Returns the reaction instances contained in the model. Varies depending on the framework.

get_stoichiometric_matrix()

Returns a 2D numpy array with the stoichiometric matrix whose metabolite and reaction indexes match the names defined in the class variables r_ids and m_ids

cobamp.wrappers.external_wrappers.normalize_boolean_expression(rule)

cobamp.wrappers.method_wrappers module

class cobamp.wrappers.method_wrappers.KShortestEFMEnumeratorWrapper(model, non_consumed, consumed, produced, subset=None, **kwargs)

Bases: cobamp.wrappers.method_wrappers.KShortestEnumeratorWrapper

Extension of the abstract class KShortestEnumeratorWrapper that takes a metabolic model as input and yields elementary flux modes.

get_linear_system()

class cobamp.wrappers.method_wrappers.KShortestEFPEnumeratorWrapper(model, subset, non_consumed=[], consumed=[], produced=[], **kwargs)

Bases: cobamp.wrappers.method_wrappers.KShortestEnumeratorWrapper

Extension of the abstract class KShortestEnumeratorWrapper that takes a metabolic model as input and yields elementary flux patterns.

get_linear_system()

class cobamp.wrappers.method_wrappers.KShortestEnumeratorWrapper(model, algorithm_type='kse_populate', stop_criteria=1, forced_solutions=None, excluded_solutions=None, solver='CPLEX', force_bounds={}, n_threads=0, workmem=None, big_m=False, max_populate_sols_override=None, time_limit=None, big_m_value=None)

Bases: object

ALGORITHM_TYPE_ITERATIVE = 'kse_iterative'

ALGORITHM_TYPE_POPULATE = 'kse_populate'

get_enumerator()

Returns an iterator that yields a single EFM or a list of multiple EFMs of the same size. Call next(iterator) to obtain the next set of EFMs.

get_linear_system()

class cobamp.wrappers.method_wrappers.KShortestMCSEnumeratorWrapper(model, target_flux_space_dict, target_yield_space_dict, **kwargs)

Bases: cobamp.wrappers.method_wrappers.KShortestEnumeratorWrapper

Extension of the abstract class KShortestEnumeratorWrapper that takes a metabolic model as input and yields minimal cut sets.

get_linear_system()

Module contents