anvi-script-kofam-accessions-to-hmms-directory
Table of Contents
You give this program one or more KOfam accession ids, and it generates an anvi'o compatible HMM directory to be used with anvi-run-hmms by extracting them from your local KEGG setup..
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Authors
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Usage
You give this program one or more KOfam accession ids, and it generates an anvi’o compatible HMM directory hmm-source to be used with anvi-run-hmms by extracting them from your local kegg-data setup.
Basic usage
You may either specify a list of KOfam accessions with --kofam-accessions-list:
anvi-script-kofam-accessions-to-hmms-directory --kofam-accessions-list K00001 K00121 \ -o PROFILE-NAME
Or a file containing this list using --kofam-accessions-file. The file should have one accession number per line:
anvi-script-kofam-accessions-to-hmms-directory --kofam-accessions-file file.txt \ -o PROFILE-NAME
Please note that the PROFILE-NAME will become the name for the HMM source when you use this HMM directory with anvi-run-hmms. So choose the output directory name accordingly, and make sure (1) it does not conflict with any existing HMM source name in your anvi’o setup, and (2) it is descriptive of the profile you are building.
If your KEGG data is not in the default location, you can specify it using --kegg-data-dir:
anvi-script-kofam-accessions-to-hmms-directory --kofam-accessions-list K00001 \ --kegg-data-dir /path/to/KEGGDATA \ -o PROFILE-NAME
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.