Incorrect output from GPRparser

[priyanka baloni]

I was implementing iMAT algorithm on HMR2 model and found that when GPRparser is used on the model (using parsedGPR = GPRparser(model) function), the parsedGPR file gives output that contains only last entry of the GPR. I tried implementing the function on ecoli model also, and again got random result.

For example:
load('ecoli_core_model');

Reaction 1: ACALD (reaction)   (b0351) or (b1241) (GPR)

Output after implementing GPRparser:
Reaction 1: ACALD (reaction)  ([] 'b0008') (Incorrect GPR as output)

In model.genes file the first entry is of 'b0008'

I went through the code but unable to figure out how is the indexing getting mixed up.

Your help will be appreciated.



 

[Thomas Pfau]

Hi,

I can't replicate this behaviour.

Could you post the results of generateSystemConfigReport() after running updateCobraToolbox?

In addition, please try to avoid using load to import models. readCbModel can import models in mat format and ensures that they are compatible with the defined model structure.
Asfor HMR:
Loading HMR can take quite some time, as the GPR format in HMR is a textual format which has to be converted to a computer readable format (i.e. the rules field needs to be created by parsing the GPR rules). Internally the COBRA toolbox relies on the rules field for functionality, as this is the only field where we can be certain of the format, and which cannot go wrong due to odd Gene Names.

Best

Thomas

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[priyanka baloni]

Hi Thomas,

I have attached the log file generated after running generateSystemConfigReport().

I tried importing the model using readCbModel and it gave correct output. Thanks for the suggestion.

[Thomas Pfau]

Hi Priyanka,

From the config report, it looks like you are working on a modified Toolbox version. This can either be due to modifications or if you stored files in the COBRA folder.
It is in general a good idea not to save additional scripts in the cobra folder, as these can interfere with the toolbox functionality.

This being said, I would advise to update the toolbox to the latest master version.

Best

Thomas