17.1.1.4.1.2. cobra.manipulation.delete

Provide functions for pruning reactions, metabolites and genes.

17.1.1.4.1.2.1. Module Contents

17.1.1.4.1.2.1.1. Classes

_GeneRemover

Class to represent a gene set remover.

17.1.1.4.1.2.1.2. Functions

prune_unused_metabolites(model: Model) → Tuple[‘Model’, List[‘Metabolite’]]

Remove metabolites not involved in any reactions.

prune_unused_reactions(model: Model) → Tuple[‘Model’, List[‘Reaction’]]

Remove reactions with no assigned metabolites, returns pruned model.

undelete_model_genes(model: Model) → None

Undo the effects of a call to delete_model_genes in place.

get_compiled_gene_reaction_rules(model: Model) → Dict[‘Reaction’, Module]

Generate a dictionary of compiled gene-reaction rules.

find_gene_knockout_reactions(model: Model, gene_list: List[‘Gene’], compiled_gene_reaction_rules: Optional[Dict[‘Reaction’, Module]] = None) → List[‘Reaction’]

Identify reactions which will be disabled when genes are knocked out.

delete_model_genes(model: Model, gene_list: List[‘Gene’], cumulative_deletions: bool = True, disable_orphans: bool = False) → None

Temporarily remove the effect of genes in gene_list.

remove_genes(model: Model, gene_list: List[‘Gene’], remove_reactions: bool = True) → None

Remove genes entirely from the model.
cobra.manipulation.delete.prune_unused_metabolites(model: Model) → Tuple['Model', List['Metabolite']][source]

Remove metabolites not involved in any reactions.

Parameters

model (cobra.Model) – The model to remove unused metabolites from.

Returns

  • cobra.Model – Input model with unused metabolites removed.

  • list of cobra.Metabolite – List of metabolites that were removed.

cobra.manipulation.delete.prune_unused_reactions(model: Model) → Tuple['Model', List['Reaction']][source]

Remove reactions with no assigned metabolites, returns pruned model.

Parameters

model (cobra.Model) – The model to remove unused reactions from.

Returns

  • cobra.Model – Input model with unused reactions removed.

  • list of cobra.Reaction – List of reactions that were removed.

cobra.manipulation.delete.undelete_model_genes(model: Model) → None[source]

Undo the effects of a call to delete_model_genes in place.

Parameters

model (cobra.Model) – The model which will be modified in place.

cobra.manipulation.delete.get_compiled_gene_reaction_rules(model: Model) → Dict['Reaction', Module][source]

Generate a dictionary of compiled gene-reaction rules.

Any gene-reaction rule expression which cannot be compiled or do not evaluate after compiling will be excluded. The result can be used in the find_gene_knockout_reactions function to speed up evaluation of these rules.

Parameters

model (cobra.Model) – The model to get gene-reaction rules for.

Returns

The dictionary of cobra.Reaction objects as keys and ast.Module objects as keys.

Return type

dict of cobra.Reaction, ast.Module

cobra.manipulation.delete.find_gene_knockout_reactions(model: Model, gene_list: List['Gene'], compiled_gene_reaction_rules: Optional[Dict['Reaction', Module]] = None) → List['Reaction'][source]

Identify reactions which will be disabled when genes are knocked out.

Parameters

  • model (cobra.Model) – The model for which to find gene knock-out reactions.

  • gene_list (list of cobra.Gene) – The list of genes to knock-out.

  • compiled_gene_reaction_rules (dict of {reaction: compiled_string},) – optional If provided, this gives pre-compiled gene-reaction rule strings. The compiled rule strings can be evaluated much faster. If a rule is not provided, the regular expression evaluation will be used. Because not all gene-reaction rule strings can be evaluated, this dict must exclude any rules which can not be used with eval (default None).

Returns

  • list of cobra.Reaction – The list of cobra.Reaction objects which will be disabled.

  • .. deprecated:: 0.22.1 – Internal function that has outlived its purpose.

cobra.manipulation.delete.delete_model_genes(model: Model, gene_list: List['Gene'], cumulative_deletions: bool = True, disable_orphans: bool = False) → None[source]

Temporarily remove the effect of genes in gene_list.

It sets the bounds to “zero” for reactions catalysed by the genes in gene_list if deleting the genes stops the reactions from proceeding.

Parameters

  • model (cobra.Model) – The model whose reaction bounds are to be set.

  • gene_list (list of cobra.Gene) – The list of genes to knock-out.

  • cumulative_deletions (bool, optional) – If True, then any previous deletions will be maintained in the model (default True).

  • disable_orphans (bool, optional) – If True, then orphan reactions will be disabled. Currently, this is not implemented (default False).

class cobra.manipulation.delete._GeneRemover(target_genes: List['Gene'], **kwargs)[source]

Bases: ast.NodeTransformer

Class to represent a gene set remover.

Parameters

target_genes (list of cobra.Gene) – A list of genes to be removed.

visit_Name(self, node: Gene) → Optional['Gene'][source]

Remove a gene.

Parameters

node (cobra.Gene) – The gene to remove.

Returns

None if gene object is in target_genes.

Return type

cobra.Gene or None

visit_BoolOp(self, node: Gene) → Optional['Gene'][source]

Rules for boolean operations.

Parameters

node (cobra.Gene) – The gene to apply rules to.

Returns

None if size of node values is less after applying rule.

Return type

cobra.Gene or None

cobra.manipulation.delete.remove_genes(model: Model, gene_list: List['Gene'], remove_reactions: bool = True) → None[source]

Remove genes entirely from the model.

This will also simplify all gene-reaction rules with the genes inactivated.

Parameters

  • model (cobra.Model) – The model to remove genes from.

  • gene_list (list of cobra.Gene) – The list of gene objects to remove.

  • remove_reactions (bool, optional) – Whether to remove reactions associated with genes in gene_list (default True).