virtool-cli

A command line tool for working with Virtool data.

Installation

pip install virtool-cli

Usage

Ref

Commands related to building, maintaining and pulling new data for reference databases.

Build

To build a reference.json file from a src directory

virtool ref build -src DIRECTORY_PATH -o OUTPUT_PATH

If you wish for the output file to be more easily readable you can specify it to be indented

virtool ref build -src DIRECTORY_PATH -i

To specify a version to include in the reference.json file

virtool ref build -src DIRECTORY_PATH -V VERSION

Repair

Fix folder-JSON name mismatches and incorrect taxid types

virtool ref repair -src DIRECTORY_PATH

taxid

Search GenBank for matching OTUs and add their taxon ids to otu.json entries in the source directory.

virtool ref taxid -src DIRECTORY_PATH

Environmental Variables

Some of the tools in the CLI make API requests to NCBI. Unauthenticated requests are are limited to 3 per second. Setting NCBI credentials in environmental variables can increase this to 10 per second.

Name	Description
NCBI_EMAIL	The e-mail address used for your NCBI account
NCBI_API_KEY	The API key associated with your NCBI account.