snpio 1.6.16

SNPio is a Python API for population genetic file processing, filtering, and analysis. It is designed to be a user-friendly tool for the manipulation of population genetic data in a variety of formats. SNPio can be used to filter data based on missingness, MAF and MAC, singletons, biallelic, and monomorphic sites. It can also generate summary statistics for population genetic analyses.

SNPio: A Python API for Population Genomic Data I/O, Filtering, Analysis, and Encoding

SNPio is a Python package designed to streamline the process of reading, filtering, encoding, and analyzing genotype alignments. It supports VCF, PHYLIP, STRUCTURE, and GENEPOP file formats, and provides high-level tools for visualization, downstream machine learning analysis, and population genetic inference.

SNPio Includes:

• File I/O (VCFReader, PhylipReader, StructureReader, GenePopReader)
• Genotype filtering (NRemover2)
• Genotype encoding for AI & machine learning applications (GenotypeEncoder)
• Population genetic statistics & Principal Component Analysis (PopGenStatistics)
• Experimental: Phylogenetic tree parsing (TreeParser)

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📖 Full Documentation

Detailed API usage, tutorials, and examples are available in the Documentation

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🔧 Installation

You can install SNPio using one of the following methods:

✅ Pip Installation

python3 -m venv snpio-env
source snpio-env/bin/activate
pip install snpio

✅ Conda Installation

conda create -n snpio-env python=3.12
conda activate snpio-env
conda install -c btmartin721 snpio

🐳 Docker

To run the Docker image interactively in a terminal, run the following commands:

docker pull btmartin721/snpio:latest
docker run -it btmartin721/snpio:latest

If you'd like to run SNPio in a jupyter notebook, instructions to do so in the docker container will be printed to the terminal.

Note: All three installation versions (pip, conda, docker) are actively maintained and kept up-to-date with CI/CD routines.

Note: SNPio supports Unix-based systems. Windows users should install via WSL.

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🚀 Getting Started

Import Modules

from snpio import (
    NRemover2, VCFReader, PhylipReader, StructureReader,
    GenePopReader, GenotypeEncoder, PopGenStatistics
)

Load Genotype Data (VCF Example)

vcf = "snpio/example_data/vcf_files/phylogen_subset14K_sorted.vcf.gz"
popmap = "snpio/example_data/popmaps/phylogen_nomx.popmap"

gd = VCFReader(
    filename=vcf,
    popmapfile=popmap,
    force_popmap=True,
    verbose=True,
    plot_format="png",
    prefix="snpio_example"
)

You can also specify include_pops and exclude_pops to control population-level filtering.

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🧪 Development Notes

To run unit all tests:

pip install snpio[dev]
pytest tests/

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🧾 License and Citation

SNPio is licensed under the GPL-3.0 License.

Please cite any publication(s) when using SNPio in your research. A manuscript is currently in development, and this section will be updated upon acceptance.

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🤝 Contributing

We welcome community contributions!

• Report bugs or request features on GitHub Issues
• Submit a pull request
• See CONTRIBUTING.md for contributing guidelines.

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🙏 Acknowledgments

Thanks for using SNPio. We hope it facilitates your population genomic research. Feel free to reach out with questions or feedback!