17.1.1.4.1.3. cobra.manipulation.modify
¶
Provide functions to modify model components.
17.1.1.4.1.3.1. Module Contents¶
17.1.1.4.1.3.1.1. Classes¶
Class to represent a gene ID escaper. |
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Class to represent a gene renamer. |
17.1.1.4.1.3.1.2. 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. |
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cobra.manipulation.modify.
_renames
= [['.', '_DOT_'], ['(', '_LPAREN_'], [')', '_RPAREN_'], ['-', '__'], ['[', '_LSQBKT'], [']', '_RSQBKT'], [',', '_COMMA_'], [':', '_COLON_'], ['>', '_GT_'], ['<', '_LT'], ['/', '_FLASH'], ['\\', '_BSLASH'], ['+', '_PLUS_'], ['=', '_EQ_'], [' ', '_SPACE_'], ["'", '_SQUOT_'], ['"', '_DQUOT_']][source]¶
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cobra.manipulation.modify.
_escape_str_id
(id_str: str) → str[source]¶ Make a single string ID SBML compliant.
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class
cobra.manipulation.modify.
_GeneEscaper
[source]¶ Bases:
ast.NodeTransformer
Class to represent a gene ID escaper.
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visit_Name
(self, node: Gene) → '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
-
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cobra.manipulation.modify.
escape_ID
(model: Model) → None[source]¶ Make all model component object IDs SBML compliant.
- Parameters
model (cobra.Model) – The model to operate on.
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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.
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visit_Name
(self, node: Gene) → 'Gene'[source]¶ Rename a gene.
- Parameters
node (cobra.Gene) – The gene to rename.
- Returns
The renamed gene object.
- Return type
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cobra.manipulation.modify.
rename_genes
(model: 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.