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mauriceccy / scobra

scobra - an extension of cobrapy
MIT License
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Can't export SBML file #13

Closed mauriceccy closed 5 years ago

mauriceccy commented 5 years ago

Problem with exporting SBML file, e.g. https://static-content.springer.com/esm/art%3A10.1038%2Fs41477-018-0112-2/MediaObjects/41477_2018_112_MOESM3_ESM.xml

Potentially because of wrong default arguments used.

ajsanjoaquin commented 5 years ago

Hi Maurice, HEXOKINASE_RXN_MANNOSE_c1 & HEXOKINASE_RXN_MANNOSE_c2 are causing the export error. When you read the file, cobra flags a warning that they are a malformed gene.

p

They produce a type error that prevents the file to be exported as sbml. The correct WriteModel arguments can be found here:

Capture

I deleted the two reactions, and I was able to export them successfully. I also read and exported an sbml file taken online. I suggest you reformat these two reactions because their format may be corrupted.