A DB-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..
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A directory of data downloaded from the KEGG database resource for use in function annotation and metabolism estimation.
It is created by running the program anvi-setup-kegg-kofams. Not everything from KEGG is included in this directory, only the information relevant to downstream programs. The most critical components of this directory are KOfam HMM profiles and the modules-db which contains information on metabolic pathways as described in the KEGG MODULES resource.
The default location of this data is in the anvi’o folder, at
You can change this location when you run anvi-setup-kegg-kofams by providing a different path to the
anvi-setup-kegg-kofams --kegg-data-dir /path/to/directory/KEGG
If you do this, you will need to provide this path to downstream programs that require this data as well.
Here is a schematic of how the kegg-data folder will look after setup:
KEGG |- MODULES.db |- ko_list.txt |- modules.keg |- HMMs | |- Kofam.hmm | |- Kofam.hmm.h3f | |- (....) | |- modules | |- M00001 | |- M00002 | |- (....) | |- orphan_data |- 01_ko_fams_with_no_threshold.txt |- 02_hmm_profiles_with_ko_fams_with_no_threshold.hmm
Typically, users will not have to work directly with any of these files, as downstream programs will interface directly with the modules-db.
However, for the curious:
modules.keg, and all files in the
modules subfolder are flat text files downloaded from the KEGG website. The data in these files are processed and organized into the modules-db for easier programmatic access.
HMMs subfolder contains a file of concatentated KOfam profiles (also originally downloaded from KEGG), as well as the indexes for this file. Some KOfam profiles do not have a score threshold in the
ko_list.txt file - these profiles and their corresponding entries from that file live in the
orphan_data directory. Please note that KOs from the
orphan_data directory will not be annotated in your contigs-db when you run anvi-run-kegg-kofams.
Edit this file to update this information.