cobra.manipulation.modify

cobra.manipulation.modify#

Provide functions to modify model components.

Attributes#

_renames

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.

Module Contents#

cobra.manipulation.modify._renames = (('.', '_DOT_'), ('(', '_LPAREN_'), (')', '_RPAREN_'), ('-', '__'), ('[', '_LSQBKT'), (']',...#
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.

rename_dict#
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.