uniref90_rxn vs. uniref90_level4ec

[Liz]

Hi,

I wanna regroup my gene family abundance values to enzyme (EC) categories, and I am following the manual section "3.3 Regrouping genes to other functional categories". 

When I try to use "--group uniref90_level4ec" I get the error msg "humann2_regroup_table: error: argument -g/--groups: invalid choice: 'uniref90_level4ec' (choose from 'uniref90_rxn', 'uniref50_rxn')". Is it a matter of versions?

One other question is: using "--group uniref90_rxn" I got the follow output:

# Gene Family   temp_Abundance-RPKs

UNGROUPED       652396.707

UNMAPPED        526848.0

1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN     45.909

1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN|g__Aerococcus.s__Aerococcus_viridans        3.401

1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN|g__Bacillus.s__Bacillus_megaterium  12.125

1-ACYLGLYCEROL-3-P-ACYLTRANSFER-RXN|g__Corynebacterium.s__Corynebacterium_jeikeium      30.382

1.1.1.127-RXN   2.963

1.1.1.127-RXN|g__Bacillus.s__Bacillus_subtilis  2.963

1.1.1.215-RXN   9.078

1.1.1.215-RXN|g__Bacillus.s__Bacillus_subtilis  9.078

1.1.1.251-RXN   2.099

1.1.1.251-RXN|g__Bacillus.s__Bacillus_megaterium        2.099

1.1.1.261-RXN   10.937

1.1.1.261-RXN|g__Bacillus.s__Bacillus_licheniformis     0.904

1.1.1.261-RXN|g__Bacillus.s__Bacillus_subtilis  10.033

1.1.1.274-RXN   44.423

1.1.1.274-RXN|g__Aerococcus.s__Aerococcus_viridans      5.274

Is there some way I can recover all the aa sequences IDs related with each E.C number in this file?

Thank you a lot,

Liz.

[Eric Franzosa]

Hi Liz,

You can install additional mapping files using the humann2_databases script. This is explained in the help section for the humann2_regroup_table script:

https://bitbucket.org/biobakery/humann2/wiki/Home#markdown-header-humann2_regroup_table

​This is the actual mapping file that tells which UniRef90s are associated with with level-4 EC terms (according to UniProt's annotations):

https://bitbucket.org/biobakery/humann2/src/tip/humann2/data/misc/map_level4ec_uniref90.txt.gz

Thanks,

Eric