anvi-import-misc-data

Populate additional data or order tables in pan or profile databases for items and layers, OR additional data in contigs databases for nucleotides and amino acids (the Swiss army knife-level serious stuff).

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Authors

Can consume

pan-db profile-db contigs-db misc-data-items-txt dendrogram phylogeny misc-data-layers-txt misc-data-layer-orders-txt misc-data-nucleotides-txt misc-data-amino-acids-txt

Can provide

misc-data-items misc-data-layers misc-data-layer-orders misc-data-nucleotides misc-data-amino-acids

Usage

This program enables extending anvi’o projects with many kinds of additional data. Additional data will extend anvio’ interactive displays, and appear in summary files, and become accessible to other anvi’o programs thorughout.

This program can add additional data for your items or layers in a pan-db or profile-db, or add additional data for your nucleotides or amino acids in a contigs-db

You also have the option to associate keys with only a specific data group, or transpose the input before processing.

Also see the program anvi-show-misc-data, anvi-export-misc-data, and anvi-delete-misc-data.

Items Data, Layers Data, and Orders

Please see this blog post for a comprehensive documentation on these misc data types.

Data groups for items

Items additional data is organized into data groups. When you import data without specifying a group, it goes into the default group. You can assign your data to a specific group using the -D flag:

In the interactive interface, each group appears as a checkbox in the Main tab, allowing you to toggle entire groups of layers on or off. Groups also provide automatic visual separation between related layers.

Several anvi’o programs automatically create named groups when they write items additional data. For instance, anvi-pan-genome creates groups like gene_cluster_stats, SCG, homogeneity, and AAI. See misc-data-items for the full list.

Data key names must be unique across all groups. If you try to import a key that already exists in another group, anvi’o will report an error. You can remove the existing key first with anvi-delete-misc-data if needed.

Nucleotides, Amino Acids, and Contigs Databases

This feature lets you import additional data about specfic residues or specific base pairs into your contigs-db. This is especially useful for strucutral analysis (so when running programs like anvi-display-structure) and will be very relevant to the InteracDome functionality when it’s added in anvi’o v7 (curious readers can take a look at this blog post).

When adding additional data, unlike with layers and items, you do not have to provide values for every single nucleotide in your database. With this program, you can easily provide data for only a select few.

Basically, you can add two types of data to your contigs database:

1. misc-data-nucleotides by providing a misc-data-nucleotides-txt. This contains information about specific nucleotides in your database.

1. misc-data-amino-acids by providing a misc-data-amino-acids-txt. This contains information about specific amino acid residues in your database

Edit this file to update this information.

Additional Resources

• A primer on anvi'o misc data tables

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.