Dear bioBakery forum,
Thanks for the awesome tools you are developing.
I am working on oral microbiome dataset and I would like to:
I have been using the latest humann3 - alpha .
Do you have the hierarchy file available for the pathways? for the genes (uniref90, GO, EC, …)
I’m not one of the developers but was recently looking at this. You can use the humann3 utility script
humann_regroup_table.py (link) to “regroup” the IDed UniRef90 genes into GO, level 4 ec, metacyc, etc, then use the humann_rename script to convert to more readable names.
I believe one of the other utility scripts will also focus on specific pathways (based on files you input), but I’m not sure which one. Maybe humann_split_stratified_table??
Thanks for your suggestions.
I am quite familiar with the
rename to map gene families to different functional informations. It seems that
humann_split_table does actually the opposite of
humann_join_tables and will not help to achieve what I am trying to! But thanks again for sharing
any help would be very much appreciated!
thanks in advance.
Sorry for missing this message. The attached file is not a part of HUMAnN but will associate MetaCyc pathways with higher-level organizational terms. More specifically, each line maps a pathway to a “taxonomy” of less to more specific categories of metabolism. I hope this helps!
map_metacyc-pwy_lineage.tsv (270.7 KB)
The map file provided by franzosa is what I am looking for in a few days before. MetaCyc pathway hierarchical structure like KEGG pathway map file? . At that time, without any reply in my topic, I created such a pathway map file for the downstream analysis. The difference between this file and mine is that I only kept the superclass1 and 2 and trimmed the longer lineage for convenience in data analysis. What you need for “Carbohydrate Degradation” is in the superclass2. I followed the naming with MetaCyc website. See the R package file2meco (GitHub - ChiLiubio/file2meco: Tranform files to the microtable object in microeco package) and data/MetaCyc_pathway_map.RData in it if it is useful.
Apologies for missing your thread - I was apparently not following the parent “community profiling” category (just the tools within it). Nice work creating the independent pathway annotation file and thanks for sharing it!
Hi Eric, hi ChiLui,
Thanks for your answer. Awsome package Chi, thanks for sharing.
I am using humann2 but am trying to do something similar and wish to focus of xenobiotic metabolism and carbohydrate metabolism pathways. Can you share exactly how you overcame this problem?
I tried regrouping the gene abundance file with GO and then rename it, but thats not exactly what I want.
Is there a mapping file for metacyc pathways that could be used for regrouping? And then renaming using metacy-name-pathway file?
Would that be the approach?
Any help would be appreciated.
Dear Eric, I’ve been using the map_metacyc-pwy_lineage.tsv in HUMAnN2 and will do the same now for HUMAnN3. I found that the file here is the same that I downloaded some years ago… Do you plan to obtain an updated version of the MeatCyc pathways lineages? Or, how did you create the first one, so that anyone potentially interested can work on it? Thanks in advance