writeSBML error

[Uri David Akavia]

Hi.

I'm having trouble writing metabolic models to SBML. If I try RECONv2.04 (the mat file, downloaded from the RECON site) and try to write it to SBML, I get various errors in  OutputSBML.

Issue #161 suggests it is a result of unsupported characters, but RECONv2.04 doesn't have them. Any suggestions? Can I help debug this issue?

Yours,

Uri David

[Uri David Akavia]

Never mind.

Apparently, writeCbModel works as long as it doesn't get a directory, only a file name.

So, basically,

writeCbModel(modelR204, 'sbml', 'RECON'); works great

writeCbModel(modelR204, 'sbml', '~/PATH/RECON'); doesn't work.

I'll see about adding the option of specifying a path some other time.

Cheers,

Uri David

[Thomas PFAU]

Hi Uri:

That's actually not a COBRA problem (I think), but a problem of either Matlab or the libSBML bindings.
~ is for some reason not recognized as you home folder. I had a similar issue once and changing it to the actual folder (i.e. with /home/user/abc instead of ~/abc works fine.

I'll have a closer look on Monday.

Best
Thomas

From: cobra-...@googlegroups.com [cobra-...@googlegroups.com] on behalf of Uri David Akavia [uridavi...@gmail.com]
Sent: 12 March 2017 03:51
To: COBRA Toolbox
Subject: Re: writeSBML error [SOLVED]

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[Thomas Pfau]

HI again,

This is indeed a problem of the libSBML bindings which use c++. And by default fopen does not recognize ~ as a placeholder for the home directory, leading to the observed effect. I'll let them know and (hopefully) this will be fixed in the next libSBML release which is due to be released at the beginning of April.

Best,

Thomas

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[Ronan M.T. Fleming]

Hi Uri,

we have been working on the SBML interface recently, so I am surprised you are having problems with it. Are you using the latest version:

https://github.com/opencobra/cobratoolbox.git

Ronan

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[Uri David Akavia]

Hi.

This was already resolved, with the help of Thomas Pfau.

Uri David

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