Microbial 'omics


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anvi-import-misc-data [program]

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).

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

Table of Contents

Provides

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

Requires or uses

genes-db 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

Usage

This program lets you bring additional information into your anvi’o databases that will appear when you run anvi-interactive.

With this, you can

  • bring additional data about your items or layers into the anvi’o interactive interface by putting it into a pan-db or profile-db
  • bring additional data about your nucleotides/amino acids into a contigs-db

You also have the option to associate keys with only a specific data group, or transpose the input before processing (in case you misformatted it).

If you no longer want to see data you’ve added with this function, you can export it as the original text file with anvi-export-misc-data and delete it from the database with anvi-delete-misc-data.

Items, Layers, and the Interactive Interface

This process, as well as the definition of an item and a layer, are described in more detail in this blog post.

Basically, you can add additional information to the interactive interface by running this program on the database you want to display and a text file containing your information. You can do this with three types of data (see their individual pages for more information on each):

  1. misc-data-items by providing a misc-data-items-txt. This contains information about each of your items in the central tree (whether those are contigs, bins, or genes), and will appear as additional concentric circles when you run anvi-interactive.

    anvi-import-misc-data -p profile-db \ -t items \ misc-data-items-txt

  2. misc-data-layers by providing a misc-data-layers-txt. This contains information about each layer (or concentric circle) of the interface (which usually correspond to your samples), and will appear as graphs in line with your circles of data (on the right, similar to how to the titles of each layer are displayed at the top) when you run anvi-interactive.

    anvi-import-misc-data -p pan-db \ -t layers \ misc-data-layers-txt

  3. misc-data-layer-orders by providing a misc-data-layer-orders-txt. This contains information about what order you want the concentric circles to be displayed in (which usually correspond to your samples), and will appear as above the misc-data-layers graphs as a tree when you run anvi-interactive.

    anvi-import-misc-data -p profile-db \ -t layer_orders \ misc-data-layer-orders-txt

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-3dev) 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.

    anvi-import-misc-data -c contigs-db \ -t nucleotides \ misc-data-nucleotides-txt

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

    anvi-import-misc-data -c contigs-db \ -t amino_acids \ misc-data-amino-acids-txt

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.