anvi-import-misc-data
Table of Contents
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).
🔙 To the main page of anvi’o programs and artifacts.
Authors
Requires
profile-db 
misc-data-items-txt 
Can use
pan-db contigs-db dendrogram 
phylogeny misc-data-layers-txt misc-data-layer-orders-txt misc-data-nucleotides-txt misc-data-amino-acids-txt
Provides
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 pan-summary, pan-graph-summary, or profile-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:
anvi-import-misc-data -p pan-db \ -t items \ -D my_analysis \ misc-data-items-txt
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:
- 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
- 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.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-import-misc-data.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
Parameters and their descriptions
TAB DELIMITED FILErequired- The input file that describes an additional data for layers or items. The expected format of this file depends on the data table you will target. This can feel complicated, but we promise it is not (you probably have a PhD or working on one, so trust us when we say "it is not complicated"). You need to read the online documentation if this is your first time with this.
-p, --pan-or-profile-dbPAN_OR_PROFILE_DB- An anvi'o pan-db or profile-db (and even genes-db or pan-graph-db in appropriate contexts).
-c, --contigs-dbCONTIGS_DB- Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-t, --target-data-tableNAMErequired- The target table is the table you are interested in accessing. Currently it can be 'items','layers', or 'layer_orders'. Please see most up-to-date online documentation for more information.
-D, --target-data-groupNAME- Data group to focus. Anvi'o misc data tables support associating a set of data keys with a data group. If you have no idea what this is, then probably you don't need it, and anvi'o will take care of you. Note: this flag is IRRELEVANT if you are working with additional order data tables.
--transpose- Transpose the input matrix file before clustering.
--just-do-it- Don't bother me with questions or warnings, just do it.
--contigs-mode- Use this flag if your binning was done on contigs instead of splits. Please refer to the documentation for help.
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.