error: printFluxVector

[bs2019]

Hi Cobra Toolbox Users,

I recently installed the R2022b matlab, cobratoolbox-master, and mosek. I could run the 'optimizeCbModel' function and get the 'FBAsolution.x' with the 'ecoli_core_model'. But, when I wanted to print the fluxes using the 'printFluxVector' function I get the following error:

>> printFluxVector(model,FBAsol.x,true)

Index in position 2 exceeds array bounds. Index must not exceed 1.

Error in printFluxVector (line 96)

labels(:,2) = pad(labels(:,2));

Any help on this issue would be highly appreciated. Thanks!!

BS

[dtusso]

Hello Everyone

I get the same error. Anyone does know how can we solve it? 

Thanks

[B. Sen]

Hi!

After I had a closer look at the script printFluxVector, I found that in line 96 if we use the following code then it prints the fba solution vector:

labels(:,1) = pad(labels(:,1));

Let me know if that solves the problem.

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[Ronan M.T. Fleming]

Hi Ben, et al,

I've repaired printFluxVector now. The update is in the master branch

https://github.com/opencobra/cobratoolbox/tree/master

Can you please test it to see if it works for you?

Regards,

Ronan

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[bs2019]

Hi Ronan,

With your repaired printFluxVector.m, it prints the fluxes when only nonZeroFlag and excFlag are set to true or false. However, when I also set the formulaFlag and gprFlag as true, I get the following error:

>> printFluxVector(model, FBA.solution.x, true,true,true,true);
Error using fopen
First input must be a file name or a file identifier.

Error in printLabeledData (line 56)
        fid = fopen(fileName, 'a');%change to append by default, in case something already there

Error in printFluxVector (line 100)
printLabeledData(labels, fluxData, 0, sortCol, fileName, headerRow)

[Ronan M.T. Fleming]

Hi Ben,

please check that input, fopen was expecting a filename.

Regards,

Ronan

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[bs2019]

Hi Ronan,

I am still getting the same error despite providing a filename as another input. Can I have a look at the line of code that works for you and prints the reaction formula and the gpr? May be I am missing out something. Thanks.

[dtusso]

Hello Ronan

It works for me printing only nonZeroFlag and excFlag.

Thank you.