[BUG] Adding unnecessary exchange reactions

[Buiboni]

Problem description

Hi,
I have an issue with the models built with CarveMe. When I load the model with cobra, it says:

Adding exchange reaction EX_12ppd__R_e with default bounds for boundary metabolite: 12ppd__R_e.
Adding exchange reaction EX_12ppd__S_e with default bounds for boundary metabolite: 12ppd__S_e.
[...]

for all the exchange reactions and then:

Ignoring reaction 'EX_12ppd__R_e' since it already exists.
Ignoring reaction 'EX_12ppd__S_e' since it already exists.
[...]

The exchange reactions are indeed in the file. When doing so cobra remove all the annotations and the bounds of the reactions. It was not the case with older version of Cobra (I could not tell which one exactly but probably 0.20 or 0.19).
I use CarveMe 1.6 (I think it does that with 1.5 too), and Cobrapy 0.29 and 0.29.1, on Linux.

Here is a model that will "do the trick". You just have to load it with the io.read_sbml_model().

Thank you for your help.
B.

Environment

Linux
CobraPy: 0.29,0.29.1
CarveMe: 1.6,1.5

[Patrickens]

Yes, I am running into the same thing; BUMP

[cdiener]

This is because those use boundary metabolites which aren't really supported by most solvers and have been discouraged for a while. The implementation here (where extra exchanges are added) was the suggestion by the SBML maintainers. See #811 for the original discussion.

I understand that this can be confusing.

I thought about having more options for SBML parsing in the Configuration singleton because there are a few related issues (clipping of ID prefixes, default solver etc) where that might help. That way one would just set a preference for the handling of boundary metabolites where "drop" would be one of them (leading to only having the original exchange reaction in the model with an empty product).

[Patrickens]

OK for the moment, I run a post-processing step in carveme where I load the model, run some other post-processing steps and save it with cobra.io, which works fine for the moment. Thanks for the speedy response!