anvi-script-hmm-to-hmm-directory
Table of Contents
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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Usage
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
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