cobra.manipulation.delete

Provide functions for pruning reactions, metabolites and genes.

Attributes

logger

Classes

_GeneRemover

Class to represent a gene set remover.

Functions

prune_unused_metabolites(→ Tuple[cobra.Model, ...)	Remove metabolites not involved in any reactions.
prune_unused_reactions(→ Tuple[cobra.Model, ...)	Remove reactions with no assigned metabolites, returns pruned model.
knock_out_model_genes(→ List[cobra.Reaction])	Disable the genes in gene_list.
delete_model_genes(→ None)	Temporarily remove the effect of genes in gene_list.
remove_genes(→ None)	Remove genes entirely from the model.

Module Contents

cobra.manipulation.delete.logger

cobra.manipulation.delete.prune_unused_metabolites(model: cobra.Model) → Tuple[cobra.Model, List[cobra.Metabolite]]

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]]

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[cobra.Gene | int | str]) → List[cobra.Reaction]

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:

list[cobra.Reaction]

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

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)

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.

target_genes

visit_Name(node: ast.Name) → ast.Name | None

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) → ast.BoolOp | ast.Name | None

Rules for boolean operations.

Parameters:

node (ast.Name) – The gene to apply rules to.

Returns:

None if size of Or node values is zero after applying rule, or size of And node values is lower after applying rule.

Return type:

ast.Name or None

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

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).