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SysBioChalmers / GECKO

Toolbox for including enzyme constraints on a genome-scale model.
http://sysbiochalmers.github.io/GECKO/
MIT License
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Error in matching the custom Kcats #291

Closed HossFir closed 1 year ago

HossFir commented 1 year ago

There is an error in the following line:

https://github.com/SysBioChalmers/GECKO/blob/ea9e2ef56673f50b764a183fbe1a6d746f64cff3/protocol.m#L116

I created the customKcats.tsv for my organism, trying to apply the customized Kcat to the ecModel, it showed the error:

Unrecognized function or variable 'kcatLast'.

Error in applyKcatConstraints (line 74) https://github.com/SysBioChalmers/GECKO/blob/983c490bd2a0106e4db9603089c8b2482008f2a9/src/geckomat/change_model/applyKcatConstraints.m#L74

Error in applyCustomKcats (line 168) https://github.com/SysBioChalmers/GECKO/blob/983c490bd2a0106e4db9603089c8b2482008f2a9/src/geckomat/change_model/applyCustomKcats.m#L168

However, this error was not raised for yeast! I have the customKcats.tsv for my organism, but it could not match the ecModel!

ae-tafur commented 1 year ago

Can you share your customKcats.tsv file ?

HossFir commented 1 year ago

Here is the link to the tsv file:

https://github.com/HossFir/Cyano/blob/main/customKcats.tsv

ae-tafur commented 1 year ago

The error is caused because reaction R537 have as GPR rule sll1056 and slr0519 and slr0520 and in custom kcats you provided only Q55843, then this is not matching. Consider to put the info with the three proteins involved in the reaction or remove the protein info and just keep the rxn id, as follow: 


Q55843 + P72644 + Q55842  | slr0520 | purQ | 5.1 | R537 | GECKO v2 manual_data.txt | 1 + 1 + 1

or 

  | slr0520 | purQ | 5.1 | R537 | GECKO v2 manual_data.txt | 1 + 1 + 1

I tested this with the model you provided in #277

In any case, this function needs to handled no any reaction match with the data in customKcats.tsv. I will fix this

HossFir commented 1 year ago

Nice, my issue was solved!