cobra.manipulation.modify
¶
Provide functions to modify model components.
Module Contents¶
Classes¶
Class to represent a gene ID escaper. |
|
Class to represent a gene renamer. |
Functions¶
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Make a single string ID SBML compliant. |
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Make all model component object IDs SBML compliant. |
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Rename genes in a model from the rename_dict. |
Attributes¶
- 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.
- 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.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.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.