You give this program one or more HMM files from hmmbuild, and it generates an anvi'o compatible HMM directory to be used with anvi-run-hmms.

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This script converts a .hmm file as formatted by HMMER3 hmmbuild to an anvi’o compatible hmm-source.

Specifying the input HMM

To start you must point the command to a list of .hmm files you’d like to include in your file hmm-source using the --hmm-list parameter. You may specify one or more files

anvi-script-hmm-to-hmm-directory --hmm-list FILE1.hmm FILE2.hmm

Specifying the input HMM source

Then you must specify a source for the HMM using --hmm-source. Here you have two options. If you specify exactly one source, that will be applied to all the .hmm files passed via --hmm-list.

anvi-script-hmm-to-hmm-directory --hmm-list FILE1.hmm FILE2.hmm --hmm-source COMMON_SOURCE

Otherwise you must specify one source per file passed to --hmm-list.

anvi-script-hmm-to-hmm-directory --hmm-list FILE1.hmm FILE2.hmm --hmm-source SOURCE1 SOURCE2

Specifying the output directory

You must specify the output directory you’d like anvi’o to save your hmm-source into using -o or --output-directory. Anvi’o will create a folder at the path you specify if it does not exist, otherwise it will exit.

anvi-script-hmm-to-hmm-directory -o path/to/output

Basic usage

Putting everything together, a basic command would look like this:

anvi-script-hmm-to-hmm-directory --hmm-list FILE1.hmm --hmm-source SOURCE1 -o output_folder

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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.