15.1.1.4.1.2. cobra.manipulation.delete
¶
15.1.1.4.1.2.1. Module Contents¶
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cobra.manipulation.delete.
prune_unused_metabolites
(cobra_model)[source]¶ Remove metabolites that are not involved in any reactions
Parameters: cobra_model (cobra.Model) – the model to remove unused metabolites from Returns: list of metabolites that were removed Return type: list
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cobra.manipulation.delete.
prune_unused_reactions
(cobra_model)[source]¶ Remove reactions that have no assigned metabolites
Parameters: cobra_model (cobra.Model) – the model to remove unused reactions from Returns: list of reactions that were removed Return type: list
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cobra.manipulation.delete.
undelete_model_genes
(cobra_model)[source]¶ Undoes the effects of a call to delete_model_genes in place.
cobra_model: A cobra.Model which will be modified in place
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cobra.manipulation.delete.
get_compiled_gene_reaction_rules
(cobra_model)[source]¶ Generates a dict of compiled gene_reaction_rules
Any gene_reaction_rule expressions which cannot be compiled or do not evaluate after compiling will be excluded. The result can be used in the find_gene_knockout_reactions function to speed up evaluation of these rules.
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cobra.manipulation.delete.
find_gene_knockout_reactions
(cobra_model, gene_list, compiled_gene_reaction_rules=None)[source]¶ identify reactions which will be disabled when the genes are knocked out
cobra_model:
Model
gene_list: iterable of
Gene
- compiled_gene_reaction_rules: dict of {reaction_id: compiled_string}
- If provided, this gives pre-compiled gene_reaction_rule strings. The compiled rule strings can be evaluated much faster. If a rule is not provided, the regular expression evaluation will be used. Because not all gene_reaction_rule strings can be evaluated, this dict must exclude any rules which can not be used with eval.
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cobra.manipulation.delete.
delete_model_genes
(cobra_model, gene_list, cumulative_deletions=True, disable_orphans=False)[source]¶ delete_model_genes will set the upper and lower bounds for reactions catalysed by the genes in gene_list if deleting the genes means that the reaction cannot proceed according to cobra_model.reactions[:].gene_reaction_rule
cumulative_deletions: False or True. If True then any previous deletions will be maintained in the model.