Pathway file at a higher level

[Nida Murtaza]

Hello everyone

I recently used HUMAnN2 pipeline and got the 3 output files (gene families, pathway abundance and coverage). 

I was wondering if there is a script where we can get pathways at level 1. Example: carbohydrate metabolism, amino acid, lipid metabolism pathways etc. I am looking to have a look at the broader picture first before going in the details as I am getting in the current pathway file (example: N-10 formyl tetrahydrofolate biosynthesis, aerobactin biosynthesis etc). Or how best to sort the output file into broader categories?

Would really appreciate any suggestions and help. 

Thank you in advance

Kind regards

Nida 

[Eric Franzosa]

We don't have any scripts for working with the MetaCyc pathway hierarchy directly. However, I have pulled out the hierarchy for other projects and am happy to share it (see attached).

Thanks,

Eric

[Nida Murtaza]

Hi Eric

Thank you, for sharing this hierarchy file. However, I am still a bit confused, how best to use this file? Or how can I pull a similar file from my data? 

I understand this might be a silly question to ask. Sorry to bother you with this. 

Thank you in advance

Nida

[shriram patel]

Hi Nida, 

If you are familiar with Excel functioning, may be vlookup function can give you what you want. Otherwise, in R there are several ways to do it (google it)...

Hope that helps!!!

Regards

[diana.mar...@gmail.com]

HI Eric,

This file is nearly exactly what I'm looking for -- but I was hoping  you could describe how you obtained it, so that the script  I set up to analyze the output of humann2 is reproducible.

Nida, if the R script I'm putting together works I'm happy to share.

Diana

[Eric Franzosa]

Hi Diana,

All of the data objects in MetaCyc (including pathways) are part of a data hierarchy. I built this file by tracing the "lineage" of each pathway up the data hierarchy to the root.

Thanks,

Eric