A simple script to generate a TAB-delimited file gene caller IDs and their HMM hits for a given HMM source.
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contigs-db hmm-source hmm-hits
This program lets you convert the hmm-hits within a contigs-db into a functions-txt.
It is similar to anvi-export-functions, except it deals specifically with hmm-hits (which are generated by anvi-run-hmms; in contrast, anvi-export-functions works with the more abstract functions artifact.
Here is an example run of this program:
anvi-script-get-hmm-hits-per-gene-call -c contigs-db \ -o path/to/functions-txt
You also have the option to specify a specific hmm-source, so that only hits from that source are outputted. For example:
anvi-script-get-hmm-hits-per-gene-call -c contigs-db \ -o path/to/functions-txt \ --hmm-source Bacteria_71
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