Hello,
I’ve created tables for UniRef90 gene families and UniRef Pathways and I’m wondering if there’s a way to link these two. In general I’m looking for some sort of mapping file that says which gene families are part of which pathways.
-Eric
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You’d have to do this as a two-step process. Under the HUMAnN pathway data folder, you’ll find a file that maps gene families (UniRefs) to MetaCyc reactions:
metacyc_reactions_level4ec_only.uniref.bz2
And then there is a separate file that defines pathways according to their component reactions and arrangement:
metacyc_structured_pathways_filtered
You can consider that a gene family contributes to a detected pathway if it maps to a RXN that is included in that pathway’s definition.
The files above can also be found here:
Hi @franzosa!
humann v3.9 user here! I am basically trying to do the same as @esmith1032 (linking UniRef90 gene families and UniRef Pathways) but cannot found the files you mention, not your link does work anymore. Could you please ajourn?
Promise to update and close the post if I find the solution on my own
UPDATE 1: I found metacyc_reactions_level4ec_only.uniref.bz2 and
metacyc_structured_pathways_filtered (found as metacyc_pathways_structured_filtered, but also metacyc_pathways_structured_filtered and metacyc_pathways_structured_filtered_v24_subreactions are available) in ~/miniforge3/envs/humann3/lib/python3.7/site-packages/humann/data/pathways/
Updated here