Scripts to update the database about enrichm HOT 7 CLOSED

Hi there,

Thank you for your interest in enrichM. I just merged an older version of the script that was used to generate those files, but the way the KEGG module definitions, and the remaining pickle files are generated remains unchanged:

7258079

you should be able to pull out what you need from there.

Thanks,

Joel

from enrichm.

Thanks @geronimp !

from enrichm.

Hey @geronimp!

I've updated the KEGG database (to release 94.0+) and Pfam (to release 33.1). I managed to update every KO/Pfam-related files (with the exception of ko00000.tsv). Would you be interested in the files?

from enrichm.

Hi @apcamargo

I'm running the tool at the moment and was wondering if there was a way for you to share the updated database files?

Best,
Sven

from enrichm.

Hey @SvenTobias-Hunefeldt

The database itself is quite large, but I can send you the updated pickle files and thresholds for the HMM KO (which I found works better than the Diamond approach to assign KOs).

You can download the newest Pfam and KEGG HMMs in the links below:
ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam33.1/Pfam-A.hmm.gz
ftp://ftp.genome.jp/pub/db/kofam/archives/2020-05-10/profiles.tar.gz

The KEGGs HMMs are in individual files, so you must concatenate them.

You should replace the pfam.hmm and ko.hmm files within the databases directory.

Let me know if you manage to do that then I'll upload the smaller files.

from enrichm.

Hi @apcamargo,

I've replaced the database files (thanks for the links!).

Also when you said hmm works better than diamond, does that relate to speed or accuracy? As I'm getting the same results from both.

from enrichm.

Here you go! Just replace the original files.

Actually, I've found that the HMM-based KO assignment works better for me. It is a bit more sensitive and, now that you downloaded a newer database, it is based on a more recent KEGG release.

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