cobra.manipulation.modify

Provide functions to modify model components.

Module Contents

Classes

_GeneEscaper

Class to represent a gene ID escaper.

_Renamer

Class to represent a gene renamer.

Functions

_escape_str_id(→ str)

Make a single string ID SBML compliant.

escape_ID(→ None)

Make all model component object IDs SBML compliant.

rename_genes(→ None)

Rename genes in a model from the rename_dict.

Attributes

_renames

cobra.manipulation.modify._renames = (('.', '_DOT_'), ('(', '_LPAREN_'), (')', '_RPAREN_'), ('-', '__'), ('[', '_LSQBKT'), (']',...[source]
cobra.manipulation.modify._escape_str_id(id_str: str) str[source]

Make a single string ID SBML compliant.

Parameters

id_str (str) – The ID string to operate on.

Returns

The SBML compliant ID string.

Return type

str

class cobra.manipulation.modify._GeneEscaper[source]

Bases: ast.NodeTransformer

Class to represent a gene ID escaper.

visit_Name(node: cobra.Gene) cobra.Gene[source]

Escape string ID.

Parameters

node (cobra.Gene) – The gene object to work on.

Returns

The gene object whose ID has been escaped.

Return type

cobra.Gene

cobra.manipulation.modify.escape_ID(model: cobra.Model) None[source]

Make all model component object IDs SBML compliant.

Parameters

model (cobra.Model) – The model to operate on.

class cobra.manipulation.modify._Renamer(rename_dict: Dict[str, str], **kwargs)[source]

Bases: ast.NodeTransformer

Class to represent a gene renamer.

Parameters

rename_dict (dict of {str: str}) – The dictionary having keys as old gene names and value as new gene names.

visit_Name(node: cobra.Gene) cobra.Gene[source]

Rename a gene.

Parameters

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

Returns

The renamed gene object.

Return type

cobra.Gene

cobra.manipulation.modify.rename_genes(model: cobra.Model, rename_dict: Dict[str, str]) None[source]

Rename genes in a model from the rename_dict.

Parameters
  • model (cobra.Model) – The model to operate on.

  • rename_dict (dict of {str: str}) – The dictionary having keys as old gene names and value as new gene names.