Pathway desciption file

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Peter Bjarke Olsen

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Feb 5, 2021, 6:06:48 AMFeb 5
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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

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Feb 5, 2021, 7:03:33 AMFeb 5
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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

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Peter Bjarke Olsen

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Feb 5, 2021, 7:44:27 AMFeb 5
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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

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