Pathway desciption file

[Peter Bjarke Olsen]

The pathways predicted by picrust2 follows the annotation from biocyc.

For example RUMP-PWY
MetaCyc formaldehyde oxidation I (biocyc.org)

It would be nice with a file linking the ID RUMP-PWY to a description. Anyone who knows if such a file exist and where ?

Best regards,

Peter

[Gavin Douglas]

Hey Peter,

There is a file with a very basic description for each pathway that is packaged with PICRUSt2. See this part of the tutorial for how to add these descriptions to your files: https://github.com/picrust/picrust2/wiki/PICRUSt2-Tutorial-(v2.3.0-beta)#add-functional-descriptions

If you just want the file it’s in the github repo at: default_files/description_mapfiles/metacyc_pathways_info.txt.gz

Cheers,

Gavin

--
You received this message because you are subscribed to the Google Groups "picrust-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to picrust-user...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/picrust-users/219c9c03-059f-4d5e-ab13-95ceb888c9adn%40googlegroups.com.

[Peter Bjarke Olsen]

Many thanks for the quick answer Gavin. Exactly what I needed. And reminder to myself: RTFM :-)

Br Peter

PS

Thanks for making this great tool available