redundant bracket in GPR rules

feiranl commented 5 years ago

Description of the issue:

Redundant brackets exist in the model.rules

Expected feature/value/output:

YGR143W or YPR159W
x(352) | x(903)

Current feature/value/output:

( YGR143W or YPR159W )
( x(352) | x(903) )

I hereby confirm that I have:

[X] Tested my code with all requirements for running the model
[X] Done this analysis in the master branch of the repository
[X] Checked that a similar issue does not exist already
[X] If needed, asked first in the Gitter chat room about the issue

feiranl commented 5 years ago

@BenjaSanchez @edkerk @hongzhonglu Should we get rid of those redundant brackets?

edkerk commented 5 years ago

These redundant brackets can indeed be removed.

BenjaSanchez commented 4 years ago

@feiranl this is actually not a problem with the model, as the rules are not stored with any brackets in the .xml file:

        <fbc:geneProductAssociation>
          <fbc:or>
            <fbc:geneProductRef fbc:geneProduct="G_YGR143W"/>
            <fbc:geneProductRef fbc:geneProduct="G_YPR159W"/>
          </fbc:or>

so it is instead a redundancy that cobratoolbox introduces, actually in all rules that have more than one gene, not just the one you mention. Note however that if you convert the model to a RAVEN model using ravenCobraWrapper.m all those redundant parenthesis go away, see below (left is COBRA, right is RAVEN):

SysBioChalmers / yeast-GEM