Eduard Kerkhoven

I agree @simas232, this should be properly resolved, also discussed in #353. To avoid confusion, I'll change this PR to draft for now.

@SPD20 Could you please attach the model as SBML or MAT file, so we can replicate what you're trying to do?

You could ZIP the file first, then you should be able to attach it. Otherwise, you can email me at [email protected].

Ok, I managed to locate the problem. It's two issues: 1. Line 384 in the DeepLoc output file has no prediction for gene `L889_g19179_t1_0.4`, which brakes the function. We'll modify...

Right, it seems like there is some issues with different sources of DeepLoc (online vs. offline) giving slightly different output (there is difference in comma vs tab-separated, naming and formatting...

@eiden309 You have been running predictLocalization, did you run into these issues? And how does the output look like that you are feeding into the function?

- `metComps` as cell array of strings would work just as well, it would reduce the speed of some function but this is probably negligble, while it is more intuitive...

@BenjaSanchez in that case, you also don't use the model-provided `rev` field, you only recreate it for one specific purpose. So if `convertToIrrev` would first recreate `rev` by the same...

@simas232 regarding `metComps`, it's not about completely abolishing it, it is about turning it into a cell array of strings, instead of numeric vector. So future `model.metComps` would be the...

Interesting proposal, should this also stored in SBML when the model is exported? If so, in which field? As far as I know, SBML L3V1 FBCv2 does not have a...