In reviewing the MetaCyc merge, I noticed some compounds were merging where they shouldn't and finally realized that I wasn't making exceptions for compounds that share the same name but don't share the same structure, it needed a simple 'elif' in Add_New_Compounds.py but of course, I had to re-run the KEGG upgrade.
Given that all of the code had already been developed and improved, I only had to checkout the old version of these files before doing so:
In reviewing the MetaCyc merge, I noticed some compounds were merging where they shouldn't and finally realized that I wasn't making exceptions for compounds that share the same name but don't share the same structure, it needed a simple 'elif' in Add_New_Compounds.py but of course, I had to re-run the KEGG upgrade.
Given that all of the code had already been developed and improved, I only had to checkout the old version of these files before doing so:
../../Biochemistry/compounds.tsv ../../Biochemistry/reactions.tsv ../../Biochemistry/Aliases/UniqueModelSEED*.txt