Comments (7)
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:
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.
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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Related Issues (20)
- Custom Database
- "xargs: illegal option -- -" leading to "No files found with .faa suffix in input directory"
- bioconda package
- There is probably a wrong version of urlib in the conda package.
- 0.5.1 run error HOT 2
- cannot open help pages/wiki HOT 1
- ERROR while classifying using custom module HOT 2
- download the database separately HOT 2
- enrichm error
- Index out of range error during enrichm annotate HOT 2
- enrichm annotate KO frequency table but all zeros HOT 3
- fuzzywuzzi missing from conda env HOT 1
- enrichM database HOT 5
- AttributeError: 'Databases' object has no attribute 'M2DEF' HOT 1
- issues with help page/wiki
- Missing KO in my ko_frequency_table.tsv
- Error receiving while generating database
- K00362 cannot assign to model M00530
- Issues with Conda installation HOT 4
- keyERROR HOT 1
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