Microbial 'omics


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anvi-update-structure-database [program]

Table of Contents

Add or re-run genes from an already existing structure database. All settings used to generate your database will be used in this program.

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

Can provide

Can consume

contigs-db structure-db

Usage

This program is used to add additional genes to or re-run the analysis of genes already within a structure-db.

For that reason, it is very similar to anvi-gen-structure-database and the parameters used to run that program (when you first generated your structure-db) will be automatically applied when you run this program. To know what MODELLER parameters are being used, you run this program on a structure-db with the flag --list-modeller-params.

To run this program, just provide a contigs-db and structure-db, and name your genes of interest (either in a file or directly). If the named genes are not already in your structure-db, they will be added to the database.

For example, if your structure-db already contains the genes with caller-IDs 1, 2 and 3, and you run

anvi-update-structure-database -c contigs-db \ -s structure-db \ --gene-caller-ids 1,4,5

Then the structural analysis for genes 4 and 5 will be added to your structure-db (assuming templates are found). Gene 1 will be ignored, since it is already present.

If instead you want to re-run the structural analysis on genes that are already in your structure-db, you’ll need to specify that by adding the flag --rerun-genes

anvi-update-structure-database -c contigs-db \ -s structure-db \ --gene-caller-ids 1,4,5 \ --rerun-genes

Now, the program will rerun the analysis for gene 1 and will still add genes 4 and 5 to the structure-db.

Both of these runs will have the same MODELLER parameters as your run of anvi-gen-structure-database. However, to get the raw outputs, you will need to use the parameter --dump-dir. You can also set a specific MODELLER program with --modeller-executable. Parameters for multi-threading would also have to be given again.

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.