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ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
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Templates/Core files have inconsistent compartment names #31

Closed tfarrah closed 7 years ago

tfarrah commented 8 years ago

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?

mmundy42 commented 8 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.

tfarrah commented 8 years ago

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"

samseaver commented 8 years ago

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:

https://help.github.com/articles/fork-a-repo/