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opencobra / cobratoolbox

The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
https://opencobra.github.io/cobratoolbox
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bug in writeSBML line 496 #2122

Open maziya opened 1 year ago

maziya commented 1 year ago

defaultSboTerm is not defined in line 496 of writeSBML function. It should be set as defaultSboTerm = 176

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rmtfleming commented 1 year ago

Fork, fix, PR.

On Mon, 5 Jun 2023 at 11:33, maziya @.***> wrote:

defaultSboTerm is not defined in line 496 of writeSBML function. It should be set as defaultSboTerm = 176

I hereby confirm that I have:

  • Tried to solve the issue on my own
  • Retried to run my code with the latest version of The COBRA Toolbox
  • [ X] Checked that a similar issue has not already been opened

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tpfau commented 1 year ago

Which version of the toolbox are you running? Line 496 of writeSBML has to do with confidence scores, (and been so for quite some time). Also for reactions the defaultRxnSboTerm is set to 176 in line 481, so I'm not sure what you are referring to.

maziya commented 1 year ago

Which version of the toolbox are you running? Line 496 of writeSBML has to do with confidence scores, (and been so for quite some time). Also for reactions the defaultRxnSboTerm is set to 176 in line 481, so I'm not sure what you are referring to.

My apologies. I have now updated the toolbox.