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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

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>, , , , , <assembly_id>, <assembly_prefix>, , <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.

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
docker build -t gaan-tool .

# Run the GAAN tool inside a Docker container
docker run -it gaan-tool [command and arguments]

Replace [command and arguments] with the actual GAAN command and its arguments.

For example:

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

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