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SysBioChalmers / ecModels

A container for all enzyme constrained models created by GECKO.
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cobrapy won't read eciML1515 because of ascii character 32 in reaction id #103

Open sulheim opened 1 year ago

sulheim commented 1 year ago

The SBML file is valid with the online validator. However, with cobrapy version 0.26.2 I get this error when I try to read the eciML1515.xml file with cobra.io.read_sbml_model:

raise ValueError('Variable names cannot contain whitespace characters. "%s" contains whitespace character "%s".' % (name, char))

This error comes from the reaction with ID __R_protein32pseudoreaction on line 61811 of the xml file. Changing this ID to e.g. R_protein_pseudoreaction__ resolves the issue.