Closed tfarrah closed 7 years ago
Yes, that is a reasonable fix. The original versions of the template files used "c0" and "e0" for compartment IDs. We later changed the IDs to "c" and "e" since a template should not reference the compartment number in a community model. We must have missed the Compartments.tsv and BiomassCompounds.tsv files in the Core template.
Thanks. Would you like me to push my changes? I'm a Github newbie so I don't know what you'd need to do to give me permission to do that. I tried pushing them but not surprisingly got the message " Permission to ModelSEED/ModelSEEDDatabase.git denied to tfarrah"
Terry, the Git approach requires you to fork the repository and submit a pull request for the project owners to merge the changes. This website explains it:
I'm using Build_Model_Template.py to create template files for the ProbModelSEED software. It has run successfully for GramNegative, GramPositive, and Microbial, but failed on Core:
Traceback (most recent call last): File "./Build_Model_Template.py", line 91, in
helper.readReactionsFile(reactionsFile, includeLinenum=False)
File "/users/tfarrah/ModelSEEDDatabase/scripts/TemplateHelper.py", line 453, in readReactionsFile
raise CompartmentNotFoundError('Compartment %s not found in current list' %(compartmentIds[cindex]))
TemplateHelper.CompartmentNotFoundError: Compartment c not found in current list
I saw that, for Core, Compartments.tsv lists compartments c0 and e0, but Reactions.tsv uses compartments c and e.
To fix, I replaced all instances of c0 with c in Compartments.tsv and BiomassCompounds.tsv
Is this a reasonable fix?