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anvi-setup-kegg-kofams [program]

Table of Contents

Download and setup KEGG KOfam HMM profiles and KEGG MODULE data.

🔙 To the main page of anvi’o programs and artifacts.

Authors

Iva Veseli

Can consume

This program seems to know what its doing. It needs no input material from its user. Good program.

Can provide

kegg-data modules-db

Usage

anvi-setup-kegg-kofams downloads and organizes data from KEGG for use by other programs, namely anvi-run-kegg-kofams and anvi-estimate-metabolism. It downloads HMM profiles from the KOfam database as well as metabolism information such as that stored in the KEGG MODULES resource. The KOfam profiles are prepared for later use by the HMMER software, and the metabolism information is made accessible to other anvi’o programs as a modules-db. This program generates a directory with these files (kegg-data), which by default is located at anvio/anvio/data/misc/KEGG/.

Default Usage

If you do not provide any arguments to this program, the KOfam profiles and KEGG information will be set up in the default KEGG data directory.

anvi-setup-kegg-kofams

How does it work? By default, this program downloads a snapshot of the KEGG databases, already converted into an anvi’o-compatible format. The snapshot is a .tar.gz archive of a KEGG data directory that was generated around the time of the latest anvi’o release.

After the default KEGG archive is downloaded, it is unpacked, checked that all the expected files are present, and moved into the KEGG data directory.

Doing it this way ensures that almost everyone uses the same version of KEGG data, which is good for reproducibility and makes it easy to share annotated datasets. The KEGG resources are updated fairly often, and we found that constantly keeping the KEGG data directory in sync with them was not ideal, because every time the data directory is updated, you have to update the KOfam annotations in all your contigs databases to keep them compatible with the current modules-db (unless you were smart enough to keep the old version of the KEGG data directory around somewhere). And of course that introduces a new nightmare as soon as you want to share datasets with your collaborators who do not have the same KEGG data directory version as you. With everyone using the same kegg-data by default, we can avoid these issues.

But the trade-off to this is that the default KEGG data version is tied to an anvi’o release, and it will not always include the most up-to-date information from KEGG. Luckily, for those who want the most updated version of KEGG, you can still use this program to generate the KEGG data directory by downloading directly from KEGG (see ‘Generating an anvi’o compatible KEGG data directory from scratch’ below).

How to set up KEGG data in a non-default location

You can specify a different directory in which to put this data, if you wish:

anvi-setup-kegg-kofams --kegg-data-dir /path/to/directory/KEGG

This is helpful if you don’t have write access to the default directory location, or if you want to keep several different versions of the KEGG data on your computer. Just remember that when you want to use this specific KEGG data directory with later programs such as anvi-run-kegg-kofams, you will have to specify its location with the --kegg-data-dir flag.

Setting up an earlier KEGG snapshot

By default, the KEGG snapshot that will be installed is the latest one, which is up-to-date with your current version of anvi’o. If, however, you want a snapshot from an earlier version, you can run something like the following to get it:

anvi-setup-kegg-kofams --kegg-data-dir /path/to/directory/KEGG --kegg-snapshot v2020-04-27

Just keep in mind that you may need to migrate the MODULES.db from these earlier versions in order to make it compatible with the current metabolism code. Anvi’o will tell you if you do.

Not sure what KEGG snapshots are available for you to request? Well, you could check out the YAML file at anvio/anvio/data/misc/KEGG-SNAPSHOTS.yaml in your anvi’o directory, or you could just give something random to the --kegg-snapshot parameter and watch anvi’o freak out and tell you what is available:

anvi-setup-kegg-kofams --kegg-snapshot hahaha

Generating an anvi’o compatible KEGG data directory from scratch

This program is also capable of downloading data directly from KEGG and converting it into an anvi’o-compatible format. In fact, this is how we generate the default KEGG archive. If you want the latest KEGG data instead of the default snapshot of KEGG, try the following:

anvi-setup-kegg-kofams --download-from-kegg

How does it work? KOfam profiles are downloadable from KEGG’s FTP site and all other KEGG data is accessible as flat text files through their API. When you run this program it will first get all the files that it needs from these sources, and then it will process them by doing the following:

  • determine if any KOfam profiles are missing bitscore thresholds, and remove those from the standard profile location so that they are not used for annotation (if you want to see these, you will find them in the orphan_data folder in your KEGG data directory)
  • concatenate all remaining KOfam profiles into one file and run hmmpress on them
  • parse the flat text file for each KEGG module and store the information into the modules-db

An important thing to note about this option is that it has rigid expectations for the format of the KEGG data that it works with. Future updates to KEGG may break things such that the data can no longer be directly obtained from KEGG or properly processed. In the sad event that this happens, you will have to download KEGG from one of our archives instead.

How do I share this data? Suppose you have been living on the edge and annotating your contigs databases with a non-default version of kegg-data, and you share these databases with a collaborator who wants to run downstream programs like anvi-estimate-metabolism on them. Your collaborator (who has a different version of kegg-data on their computer) will likely get version errors as detailed on the anvi-estimate-metabolism help page.

In order for your collaborator to be able to work with your dataset, they need to have the same kegg-data version as you did when you ran anvi-run-kegg-kofams. If you are very lucky and KEGG has not been updated since you set up your kegg-data, they may be able to run anvi-setup-kegg-kofams -D to get it. But if not, there are a few options for you to share your version of kegg-data:

  1. You could send them your KEGG data directory. First, run tar -czvf kegg_archive.tar.gz ./KEGG on the data directory to compress and archive it before sending it over (this command must be run from its parent directory so that the archive has the expected directory structure when it is unpacked). Then your collaborator can just run anvi-setup-kegg-kofams --kegg-archive kegg_archive.tar.gz --kegg-data-dir ./KEGG_ARCHIVE and be good to go. They would just have to use --kegg-data-dir ./KEGG_ARCHIVE when running downstream programs. The problem here is that even the archived kegg-data is quite large, ~4-5GB, and may be unfeasible for you to send.
  2. You could share with your collaborator just the modules-db. If all they want to do is to run anvi-estimate-metabolism on databases annotated by your version of the KEGG data directory, this should be all they need. They would need to pass the folder containing your modules-db to anvi-estimate-metabolism using the --kegg-data-dir parameter.
  3. If your collaborator also wants to be able to annotate other databases with your version of kegg-data, then they need to have the KOfam profiles as well. You can send them your modules-db and have them download the KOfam profiles most similar to the ones you have from the KOfam archives (which are labeled by date). Then they would have to essentially construct their own KEGG data directory by copying the structure of the default one and putting the downloaded files (and the modules-db you sent them) into the correct locations. The KOfam profiles must be concatenated into a Kofam.hmm file and hmmpress must be run on that file to generate the required indices for hmmsearch. Your collaborator must also have the ko_list.txt file (which should be downloaded with the profiles) in the right spot. Then they could pass their makeshift KEGG data directory to anvi-run-kegg-kofams using --kegg-data-dir, and they should be golden. (A word of warning: they may want to remove KOs without bitscore thresholds in the ko_list.txt before concatenating the profiles, otherwise they will likely get a lot of weak hits for these KOs.)

Set up from archived KEGG data

If you have an archive (.tar.gz) of the KEGG data directory already on your computer (perhaps a colleague or Meren Lab developer gave you one), you can set up KEGG from this archive instead:

anvi-setup-kegg-kofams --kegg-archive KEGG_archive.tar.gz

This works the same way as the default, except that it bypasses the download step and instead uses the archive you have provided with --kegg-archive.

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.