GWAS Association Tools

A command-line tool for genomic-wide association studies (GWAS) data validation and analysis.

Features

• Validate:
  • Input: File path of GWAS Submission template that contains top associations
  • Output: Validation report of top associations

Installation

Install from PyPI:

pip install gwas-assoc-tools

Usage

# Basic validation command
gwas-assoc validate <template excel file path>

# For help
gwas-assoc --help
gwas-assoc validate --help

Development

Setup

# Install uv (if not already installed)
curl -LsSf https://astral.sh/uv/install.sh | sh

# Install dependencies
uv sync --all-groups

# Activate virtual environment
source .venv/bin/activate

Building and Installation

# Build the package (creates .whl and .tar.gz in dist/)
uv build

# Install your new package in development mode
uv sync --all-groups

Release

Publishing is done by creating a GitHub Release. The release workflow builds the package with uv and publishes to PyPI using trusted publishing, so no local PyPI credentials or GitHub secrets are needed.

Before the first release, configure the PyPI project gwas-assoc-tools with a GitHub trusted publisher:

• Owner: EBISPOT
• Repository: gwas-assoc-tools
• Workflow: publish.yml
• Environment: pypi

Configure the matching GitHub environment pypi; add reviewer protection if the maintainers want manual approval.

Testing

TODO

Running with Real Files

# Run the CLI command through uv
# For failed test file
uv run gwas-assoc validate ./tests/test_fail.xlsx
# For successful test file
uv run gwas-assoc validate ./tests/test_success.xlsx


# Or after activating the shell
source .venv/bin/activate
# For failed test file
gwas-assoc validate ./tests/test_fail.xlsx
# For successful test file
gwas-assoc validate ./tests/test_success.xlsx

Dependency Management

# Add a new dependency
uv add new-package

# Add a development dependency
uv add --group dev pytest-mock

# Check for dependency updates
uv lock --dry-run --upgrade

# Update dependencies
uv lock --upgrade

Code Quality

# Run formatting
uv run black .
uv run isort .

# Run linting
uv run ruff check .

# Run type checking
uv run mypy src

# Run all formatting checks
uv run pre-commit run --all-files

Documentation

Please find the Confluence page here: https://embl.atlassian.net/wiki/spaces/GOCI/pages/57606184/GWAS+Associations+Tools

License

License