Genome Assembly and Gene Model Identifier Tool

This command-line tool facilitates the creation and validation of genome assembly and gene model identifiers based on specific patterns. It is part of the AgBioData Genome Assembly and Annotation Nomenclature Working Group.

Requirements

• Python 3.x
• Docker (optional, for containerized usage)

Installation

To use GAAN, you need to install its dependencies. We recommend using Poetry for managing the project dependencies.

Poetry Installation

If you don't have Poetry installed, you can do so by following the instructions on the official Poetry website.

Install Dependencies

Once Poetry is installed, navigate to the project directory and run the following command to install the dependencies:

poetry install

Usage

GAAN provides command-line functionality for creating and validating genome assembly and gene model identifiers. Here are some examples of how to use GAAN:

Create Genome Assembly Identifier

poetry run gaan create-assembly <tol_id> <sample_identifier> <consortium> <version> <subversion> --optional <optional>

Validate Genome Assembly Identifier

poetry run gaan validate-assembly <assembly_id>

Create Gene Model Identifier

poetry run gaan create-gene-model <assembly_prefix> <entity> <id_number>

Validate Gene Model Identifier

poetry run gaan validate-gene-model <gene_model_id>

Replace the placeholders <tol_id>, <sample_identifier>, <consortium>, <version>, <subversion>, <optional>, <assembly_id>, <assembly_prefix>, <entity>, <id_number>, and <gene_model_id> with your specific values.

For more information and options, you can use the --help flag with any of the commands, for example:

poetry run gaan create-assembly --help

Examples

For more examples, refer to the usage section above.

Running Tests

You can run unit tests to ensure everything is working correctly. The test suite is built using Python's unittest.

Running Tests without Docker

To run tests without Docker, use the following command:

poetry run env PYTHONPATH=./src python -m unittest test_gaan.py

This will run the tests defined in test_gaan.py using the unittest framework.

Running Tests with Docker

If you prefer to run tests inside a Docker container, follow these steps:

1. Build the Docker Image

   First, build the Docker image:

   docker build -t gaan-tool .

2. Run the Tests Inside Docker

   Then, run the tests using the Docker container:

   docker run -it --entrypoint "poetry run env PYTHONPATH=./src python -m unittest test_gaan.py" gaan-tool

This will run the unit tests in the container using the same command as when running locally.

Using Docker (Optional)

If you prefer to use Docker, you can build a Docker image locally. Ensure you have Docker installed on your machine.

Build the Docker Image

To build the Docker image, run the following command in the project directory:

docker build -t gaan-tool .

Run GAAN Tool Inside Docker

To run the GAAN tool inside the Docker container, use the following syntax:

docker run -it gaan-tool [command and arguments]

For example:

docker run -it gaan-tool create-assembly ABC123 Sample1 ProjectX 1 0

Note: The Docker image is built locally and is not pushed to a container registry. This approach is suitable for local usage.