Add or remove entries in a contigDB hmm_hits table..
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
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%:
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.