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Project description
PLINKFORMMATER
This repository is designed to transform genotype data from the Muster SNPs/download endpoint into PLINK-compatible data, which can then be processed by PyLMM. The primary aim is to facilitate genomic data transformation for linear mixed models. This tool should, in theory, also work with GEMMA and other software that consumes standard PLINK file formats, though it has been primarily tested with PyLMM.
Getting Started
Prerequisites
To use this repository, you must have the following dependencies installed:
- Python 3.8 or above
- PLINK 2.0
- Poetry
Install dependencies:
poetry install
Activate virtual environment:
poetry shell
Install PLINK:
You can download PLINK from the official website. Ensure the PLINK executable is in your system's PATH, or you can specify the path to the PLINK binary in your environment settings.
To verify PLINK installation, run:
plink2 --version
Tests
To run tests run the following command:
pytest -s tests
Publishing to Pypi
- Update version
poetry version patch
- Build any changes
poetry build
- Set the correct PyPI repository URL
poetry config repositories.pypi https://upload.pypi.org/legacy/
- Set API token
poetry config pypi-token.pypi pypi-YourActualTokenHere
- Publish
poetry publish
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