HUMAnN 3 uses MetaCyc for the pathway definitions. In the code, humann/modules.py at master · biobakery/humann · GitHub it looks like it is using some annotation of the reactions as to whether they are required or optional components of the pathway. From where does this annotation originate? In MetaCyc, at least on their website (example), I can’t find reactions in a pathway characterized this way, so I am curious. Does anyone know?
Sorry for the late reply - this information is parsed out of the raw MetaCyc pathway definition files that one can download with a MetaCyc subscription.
Is the code that you use to parse the MetaCyc definition files available anywhere?
Unfortunately not at the moment - it’s part of an internal “HUMAnN maintenance” repository. We can look into the possibility of making this repository public as part of a future major HUMAnN release.