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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anvi-display-metabolism anvi-estimate-metabolism anvi-run-kegg-kofams
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.
Programs that rely on this data directory include anvi-run-kegg-kofams and anvi-estimate-metabolism.
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.