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¶
Class to represent a gene set remover. |
17.1.1.4.1.2.1.2. Functions¶
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Remove metabolites not involved in any reactions. |
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Remove reactions with no assigned metabolites, returns pruned model. |
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Undo the effects of a call to delete_model_genes in place. |
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Generate a dictionary of compiled gene-reaction rules. |
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Identify reactions which will be disabled when genes are knocked out. |
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Temporarily remove the effect of genes in gene_list. |
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Remove genes entirely from the model. |
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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.
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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.
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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.
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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
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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.
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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).
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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.
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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
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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
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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).