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Direct gene.id modification warning message. #1424

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Direct gene.id modification warning message. #1424

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13 changes: 13 additions & 0 deletions src/cobra/core/gene.py
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Original file line number Diff line number Diff line change
Expand Up @@ -221,6 +221,19 @@ def __init__(self, id: str = None, name: str = "", functional: bool = True) -> N
super().__init__(id=id, name=name)
self._functional = functional

@property
def id(self) -> str:
return super().id

@id.setter
def id(self, new_id) -> None:
warnings.warn(
"Direct modification of gene.id is discouraged and can lead to unexpected gene duplications. "
"Use cobra.manipulation.modify.rename_genes to safely rename genes.",
UserWarning
)
super(Gene, self.__class__).id.fset(self, new_id)
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As Moritz said, better not even set it but throw an error with the same message instead of a warning.


@property
def functional(self) -> bool:
"""Flag indicating if the gene is functional.
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