anvi-script-add-default-collection

Authors
Requires
Can use
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

A script to add a 'DEFAULT' collection in an anvi'o pan or profile database with either (1) a single bin that describes all items available in the profile database, or (2) as many bins as there are items in the profile database wher every item has its own bin. The former is the default behavior that will be useful in most instances where you need to use this script. The latter is most useful if you are Florian and/or have something very specific in mind..

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Authors

A. Murat Eren (Meren)

Requires

profile-db

Can use

pan-db contigs-db

Provides

collection bin

Usage

This program adds a ‘default’ collection and bin to your pan-db or profile-db and contigs-db that describes every item in your database.

This way, you can perform anvi’o tasks that require a collection or a bin even if you do not have a particular collection for your data, or all items in your database represent a meaningful bin (such as every contig in a contigs-db that represents a single genome).

As an example, see this program in action in the Infant Gut Tutorial where it is used to run anvi-interactive on a genome in ‘gene mode’.

Run in its simples form,

anvi-script-add-default-collection -c contigs-db \ -p profile-db

the program will add a new collection into the profile database named DEFAULT, which will contain a single bin that describes all items in the database named EVERYTHING. You can set these default names to your liking using additional parameters:

anvi-script-add-default-collection -c contigs-db \ -p profile-db \ -C MY_COLLECTION \ -b MY_BIN

Also see related programs, anvi-show-collections-and-bins and anvi-delete-collection.

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-script-add-default-collection.

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

anvi-script-add-default-collection [-h] -p PAN_OR_PROFILE_DB [-c CONTIGS_DB] [-C COLLECTION_NAME] [-b BIN_NAME] [--bin-each-item-separately]

Parameters and their descriptions

DATABASE INPUTS Provide a profile-, gene-, or pan-db, and if relevant, also a contigs-db here

-p, --pan-or-profile-db PAN_OR_PROFILE_DB required: An anvi'o pan-db or profile-db (and even genes-db or pan-graph-db in appropriate contexts).
-c, --contigs-db CONTIGS_DB: Anvi'o contigs database generated by 'anvi-gen-contigs-database'

COLLECTION NAME Go with the flow or be a rebel

-C, --collection-name COLLECTION_NAME: Name for the new collection. If you don't provide any then it will be named "DEFAULT". Default: DEFAULT

BINS You either provide a bin name for everything, or let every item be their own bins.

-b, --bin-id BIN_NAME: Name for the new bin. If you don't provide any then it will be named "EVERYTHING". Default: EVERYTHING
--bin-each-item-separately: If you declare this flag every item in your database will have its own bin (which is crazy, but may be necessary).

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.