psamm.randomsparse
– Find a random minimal network of model reactions¶
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class
psamm.randomsparse.
ReactionDeletionStrategy
(model, reaction_set=None)¶ Deleting reactions strategy class.
When initializing instances of this class,
get_exchange_reactions()
can be useful if exchange reactions are used as the test set.
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class
psamm.randomsparse.
GeneDeletionStrategy
(model, gene_assoc)¶ Deleting genes strategy class.
When initializing instances of this class,
get_gene_associations()
can be called to obtain the gene association dict from the model.
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psamm.randomsparse.
get_gene_associations
(model)¶ Create gene association for class
GeneDeletionStrategy
.Return a dict mapping reaction IDs to
psamm.expression.boolean.Expression
objects, representing relationships between reactions and related genes. This helper function should be called when creatingGeneDeletionStrategy
objects.Parameters: model – psamm.datasource.native.NativeModel
.
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psamm.randomsparse.
get_exchange_reactions
(model)¶ Yield IDs of all exchange reactions from model.
This helper function would be useful when creating
ReactionDeletionStrategy
objects.Parameters: model – psamm.metabolicmodel.MetabolicModel
.
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psamm.randomsparse.
random_sparse
(strategy, prob, obj_reaction, flux_threshold)¶ Find a random minimal network of model reactions.
Given a reaction to optimize and a threshold, delete entities randomly until the flux of the reaction to optimize falls under the threshold. Keep deleting until no more entities can be deleted. It works with two strategies: deleting reactions or deleting genes (reactions related to certain genes).
Parameters: - strategy –
ReactionDeletionStrategy
orGeneDeletionStrategy
. - prob –
psamm.fluxanalysis.FluxBalanceProblem
. - obj_reaction – objective reactions to optimize.
- flux_threshold – threshold of max reaction flux.
- strategy –
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psamm.randomsparse.
random_sparse_return_all
(strategy, prob, obj_reaction, flux_threshold)¶ Find a random minimal network of model reactions.
Given a reaction to optimize and a threshold, delete entities randomly until the flux of the reaction to optimize falls under the threshold. Keep deleting until no more entities can be deleted. It works with two strategies: deleting reactions or deleting genes (reactions related to certain genes).
Parameters: - strategy –
ReactionDeletionStrategy
orGeneDeletionStrategy
. - prob –
psamm.fluxanalysis.FluxBalanceProblem
. - obj_reaction – objective reactions to optimize.
- flux_threshold – threshold of max reaction flux.
- strategy –