anvi-show-misc-data
Table of Contents
Show all misc data keys in all misc data tables.
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Can use
Provides
This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.
Usage
This program lists the additional data that is stored within a pan-db, profile-db or contigs-db. This is data that can be imported with anvi-import-misc-data and is displayed in the interactive interface.
When run, this program will output to the terminal a list of all additional data tables that are stored within the database. If you want to export a specific element of these as a text file, see anvi-export-misc-data.
What is displayed?
When running on a profile-db or pan-db, the output will display the following types of data:
- misc-data-items
- misc-data-layers
- misc-data-layer-orders (by default, this will include orders like
abundanceandmean_coverage (newick))
When running on a contigs-db, the output will display the following types of data:
These have no default values and will only contain data that has been imported with anvi-import-misc-data.
You also have the option to specify a specific kind of additional data table with -t. For example, to view only misc-data-items in a profile-db, just call
anvi-show-misc-data -p profile-db \ -t items
Similarly to importing and exporting additional data tables, you can also focus on a specific data group with the parameter -D.
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-show-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
-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-tableNAME- 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.
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.