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 Poetry (if not already installed)
curl -sSL https://install.python-poetry.org | python3 -

# Install dependencies
poetry install

# Activate virtual environment
poetry shell

Building and Installation

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

# Install your new package in development mode
poetry install

Testing

TODO

Running with Real Files

# Run the CLI command through Poetry
poetry run gwas-assoc validate ./tests/snp_validator.xlsx

# Or after activating the shell
poetry shell
gwas-assoc validate ./tests/snp_validator.xlsx

Dependency Management

# Add a new dependency
poetry add new-package

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

# Check for dependency updates
poetry update --dry-run

# Update dependencies
poetry update

Code Quality

# Run formatting
poetry run black .
poetry run isort .

# Run linting
poetry run ruff check .

# Run type checking
poetry run mypy src

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

License

License