anvi-setup-pfams

Authors
Requires
Provides
Usage

Set up Pfams data

Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Download and setup Pfam data from the EBI.

🔙 To the main page of anvi’o programs and artifacts.

Authors

Iva Veseli

Özcan C. Esen

Requires

This program seems to know what its doing. It needs no input material from its user. Good program.

Provides

pfams-data

Usage

This program downloads and organizes a local copy of the data from EBI’s Pfam database for use in function annotation. This program generates a pfams-data artifact, which is required to run the program anvi-run-pfams.

Set up Pfams data

anvi-setup-pfams

By default, this data is stored at anvio/data/misc/Pfam. To set up this data in a non-default location, run

anvi-setup-pfams --pfam-data-dir path/to/location

If you already have a pfams-data artifact and are trying to redownload this data, run

anvi-setup-pfams --reset

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-setup-pfams.

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-setup-pfams [-h] [--pfam-data-dir PFAM_DATA_DIR] [--reset] [--pfam-version PFAM_VERSION]

Parameters and their descriptions

options

--pfam-data-dir PFAM_DATA_DIR: The directory for Pfam data to be stored. If you leave it as is without specifying anything, the default destination for the data directory will be used to set things up. The advantage of it is that everyone will be using a single data directory, but then you may need superuser privileges to do it. Using this parameter you can choose the location of the data directory somewhere you like. However, when it is time to run Pfam, you will need to remember that path and provide it to the program.
--reset: This program by default attempts to use previously downloaded files in your Pfam data directory if there are any. If something is wrong for some reason you can use this to tell anvi'o to remove everything, and start over.
--pfam-version PFAM_VERSION: By default, the most current version available will be downloaded. If you have specific tastes for a different version, you can provide it here. For example, `31.0`. Here are all possible versions: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/

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.