cobra.manipulation.delete
¶
Provide functions for pruning reactions, metabolites and genes.
Module Contents¶
Classes¶
Class to represent a gene set remover. |
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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Disable the genes in gene_list. |
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Temporarily remove the effect of genes in gene_list. |
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Remove genes entirely from the model. |
Attributes¶
- cobra.manipulation.delete.prune_unused_metabolites(model: cobra.Model) Tuple[cobra.Model, List[cobra.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: cobra.Model) Tuple[cobra.Model, List[cobra.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.knock_out_model_genes(model: cobra.Model, gene_list: Iterable[Union[cobra.Gene, int, str]]) List[cobra.Reaction] [source]¶
Disable the genes in gene_list.
It sets the bounds to “zero” for reactions catalysed by the genes in gene_list if deleting the genes would stop the reactions from proceeding.
The changes are reverted upon exit if executed within the model as context.
- 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.
- Returns
A list of cobra.Reactions that had the bounds turned to zero.
- Return type
- cobra.manipulation.delete.delete_model_genes(model: cobra.Model, gene_list: Union[List[cobra.Gene], Set[cobra.Gene], List[str], Set[str]], 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). Unused, ignored.
disable_orphans (bool, optional) – If True, then orphan reactions will be disabled. Currently, this is not implemented (default False). Unused, ignored.
: (.. deprecated) – 0.25: Use cobra.manipulation.knock_out_model_genes to simulate knockouts and cobra.manipulation.remove_genes to remove genes from the model.
See also
knock_out_model_genes
,remove_model_genes
- class cobra.manipulation.delete._GeneRemover(target_genes: Set[cobra.Gene], **kwargs)[source]¶
Bases:
ast.NodeTransformer
Class to represent a gene set remover.
- Parameters
target_genes (list or set of cobra.Gene) – A set of genes to be removed.
- visit_Name(node: ast.Name) Optional[ast.Name] [source]¶
Remove a gene.
- Parameters
node (ast.Name) – The gene to remove.
- Returns
None if gene object is in target_genes.
- Return type
cobra.Gene or None
- visit_BoolOp(node: ast.BoolOp) Optional[Union[ast.BoolOp, ast.Name]] [source]¶
Rules for boolean operations.
- cobra.manipulation.delete.remove_genes(model: cobra.Model, gene_list: Union[List[cobra.Gene], Set[cobra.Gene], List[str], Union[str]], 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 or gene ids) – The list of gene objects to remove.
remove_reactions (bool, optional) – Whether to remove reactions associated with genes in gene_list (default True).