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Introduction to the refget Python package

This package provides several things. In the following pages, you'll find tutorials that will walk you through:

Package components: Functions, Clients, and Agents

In these docs, you will find how-to guides describing these components:

  1. Local functions to compute digests. The refget package provides a Python interface to fast rust-based implementations of GA4GH digests for both sequences and sequence collections. If you have a representation of your sequences, such as a FASTA file or some other representation, you can use these standalone functions to compute the GA4GH digests for individual sequences or collections from Python.

  2. Clients are for interacting with a remote Refget API. If you want to use a remote refget service in your application, you can use refget Clients. There is a refget.SequenceClient object for operating with a refget sequences API, and a refget.SequenceCollectionClient for interacting with a refget sequence collections API.

  3. Agents are for interacting with a database to produce an API. If you want to create a refget service, or otherwise host your own refget database, then you can use refget Agents. The refget.RefgetDBAgent is the primary interface for creating, updating, and interacting with a SQL-backed server for storing refget sequences or collections.

  4. API router. The package also includes a simple router that implements the refget sequences API. You can attach this router to an existing FastAPI service to deploy your own sequence collections API.

  5. Compliance tests. The testing suite provides a compliance test to evaluate a remote API instance. Use this to confirm that you are implementing the sequence collections standard correctly.

  6. Command-line interface. The refget command provides some convenient functions (beta).