Microbial 'omics


Brought to you by

anvi-script-filter-hmm-hits-table [program]

Add or remove entries in a contigDB hmm_hits table..

See program help menu or go back to the main page of anvi’o programs and artifacts.

Table of Contents

Can provide

contigs-db hmm-hits

Can consume

contigs-db hmm-source hmm-hits

Usage

This program is for filtering a hmm-source from a hmm-hits in a contigs-db using HMM alignment parameters such as query-coverage and target-coverage. Briefly, the program will remove all records from an hmm-source in the hmm-hits then import a new hmm-hits table into the contigs-db that was filtered to your specifications. At the moment, this tool is only designed to work with hmmsearch with protein sequences. The --domtblout can be produced from running anvi-run-hmms with your hmm-source of interest and using the --domtblout parameter AND hmmsearch as the program.

To list available hmm-source in a database:

anvi-script-filter-hmm-hit-table -c contigs-db \ --list-hmm-sources

Make --domtblout with anvi-run-hmms

anvi-run-hmms -c contigs-db \ -I Bacteria_71 \ --just-do-it \ --hmmer-program hmmsearch \ --hmm-domain-tblout-path hmmsearch

Then you can filter out hits using query or target coverage! Here’s an example where we can filter out hmm_hits with a target-coverage less than 90%:

anvi-script-filter-hmm-hit-table -c contigs-db \ --hmm-source hmm-source \ --domtblout hmmsearch_domtable \ --target-coverage 0.9

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.