Programmatically delete Frames

pathway-tools

asked 2019-04-09 03:16:15 -0500

Anonymous

Dear,

Pathway Tools typically overpredicts the number of pathway, reaction and metabolite frames that should be linked to a specific microorganism.

As part of the curation process, I have detached genes from reactions, ommitted pathays, etc.. But now I find myself with a lot of empty frames. For example, by deleting a pathway the underlying pathway class is not deleted. This has still to be done manually afterwards, which is time-consuming.

Is there a way to programmatically delete these (empty) frames, e.g. using PythonCyc?

Kind regards, Rudy

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answered 2019-04-10 16:30:34 -0500

Peter Karp
201

Hello, It sounds like you are performing the deletions you listed via the edit menu operations.

We intentionally leave the pathway classes present even after all of their pathways are deleted, in part so that if new pathways are later added for that class, the class is there to put them under. We don't consider it problematic to have pathway classes that contain no instances.

You can probably delete the classes by using API calls to delete-frame, e.g., delete-frame(class-id)

However, it's quite possible that our schema upgrade code will add the deleted classes back in the next time you upgrade to a new version of Pathway Tools!

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