A simple script to generate a TAB-delimited file that reports the frequency of HMM hits for a given HMM source across contigs databases.
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external-genomes internal-genomes hmm-source hmm-hits
This program lets you look at the hmm-hits from a single hmm-source across multiple genomes or bins, by creating a hmm-hits-across-genomes-txt.
For a simlar program that reports function hits across genomes, see anvi-script-gen-function-matrix-across-genomes.
The input of this program can be either an internal-genomes or an external-genomes.
Here are two example run on an internal-genomes:
anvi-script-gen-hmm-hits-matrix-across-genomes -i internal-genomes \ --hmm-source Bacteria_71 \ -o output.txt
To list the hmm-sources common to the datasets that you’re analyzing, just add the flag
--list-hmm-sources, as so:
anvi-script-gen-hmm-hits-matrix-across-genomes -e external-genomes \ --list-hmm-sources
Edit this file to update this information.
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.