anvi-script-pfam-accessions-to-hmms-directory
Table of Contents
You give this program one or more PFAM accession ids, and it generates an anvi'o compatible HMM directory to be used with anvi-run-hmms.
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Authors
Requires
Provides
Usage
You give this program one or more PFAM accession ids, and it generates an anvi’o compatible HMM directory hmm-source to be used with anvi-run-hmms by downloading them from the PFAM database.
Basic usage
You may either specify a list of PFAM accessions with --pfam-accessions-list:
anvi-script-pfam-accessions-to-hmms-directory --pfam-accessions-list PF00001 PF00002 \ -o PROFILE-NAME
Or a file containing this list using --pfam-accessions-file. The file should have one accession number per line:
anvi-script-pfam-accessions-to-hmms-directory --pfam-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.
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.