Microbial 'omics


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anvi-script-get-hmm-hits-per-gene-call [program]

Table of Contents

A simple script to generate a TAB-delimited file gene caller IDs and their HMM hits for a given HMM source.

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)

Can consume

contigs-db hmm-source hmm-hits

Can provide

functions-txt

Usage

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

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.