RefGenConf provides a standardized configuration object for reference genome assemblies. It enables robust and centralized management of paths to reference genome assets, ensuring consistency for bioinformatics tools. The current version is 0.13.1, and the project maintains an active development and release cadence.
pip install refgenconfVerified import paths — ran on the pinned version, not inferred.
This example demonstrates how to initialize RefGenConf with a configuration file and retrieve paths to specific assets. It includes setup for a temporary config file for immediate execution. In practice, users typically rely on a `refgenie.yaml` file managed by the `refgenie` command-line tool.
Use `refgenie upgrade` (if applicable with your `refgenie` version) or manually update your `refgenie.yaml` to conform to the latest schema. Refer to the official RefGenConf/Refgenie documentation for schema changes.
Ensure `refgenie` is initialized by running `refgenie init` in your terminal. If using a custom path, explicitly provide it during `RefGenConf` initialization (e.g., `RefGenConf(filepath='/path/to/my_refgenie.yaml')`).
Use `refgenie list` in your terminal or inspect your `refgenie.yaml` file to verify the exact names of genomes and assets. Ensure your code uses these names precisely.
Initialize `refgenie` by running `refgenie init` in your terminal. If you intend to use a different file, pass its path explicitly to `RefGenConf(filepath='your/custom/path.yaml')`.
Run `refgenie upgrade` to attempt an automatic migration. If that doesn't work, review the RefGenConf documentation for the correct schema or regenerate the configuration by re-initializing `refgenie` and adding assets.
Check your `refgenie.yaml` file or use `refgenie list` to confirm the exact names of registered genomes and assets. Ensure your Python code uses these names precisely as they appear in the configuration.