getECfromGEM fails in light_ecModel tutorial

[kylo610]

I want to build a light ECmodel, after i finish modelAdapter and make ECmodel use:[ecModel, noUniprot] = makeEcModel(model, true); then i use : ecModel = getECfromGEM(ecModel); Then the error print: The model has no model.eccodes field. ThemakeEcModel(model, true) step should be converting a GEM to an ECmodel, right? Why is it showing that the model.eccodes field is missing? I didn't encounter this problem when I used other microorganisms to build the ecmodel before, and the code was the same. I'm looking forward to reply, think you very much.

[edkerk]

makeEcModel indeed converts the GEM into a rudimentary ec-model structure. This however does not generate a model.eccodes field.

getECfromGEM only works if the ecModel has the ecModel.eccodes, which it won't if the starting GEM did not have a model.eccodes field.

You did not run into this issue with other microorganisms, if their models contains model.eccodes fields.

As alternative, EC can be gathered by the function ecModel = getECfromDatabase(ecModel,); as detailed in Step 17 of the protocol.

Note that the light_ecModel example script only refers to getECfromGEM. But whether you use that function and/or getECfromDatabase has nothing to with generating full or light ec-models, it just depends on what source of EC information is available and you want to use to construct the ec-model.