# 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)
---
## 📖 Full Documentation
Detailed API usage, tutorials, and examples are available in the [Documentation](https://snpio.readthedocs.io/en/latest/)
---
## 🔧 Installation
You can install SNPio using one of the following methods:
### ✅ Pip Installation
```bash
python3 -m venv snpio-env
source snpio-env/bin/activate
pip install snpio
```
### ✅ Conda Installation
```bash
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:
```bash
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.
---
## 🚀 Getting Started
### Import Modules
```python
from snpio import (
NRemover2, VCFReader, PhylipReader, StructureReader,
GenePopReader, GenotypeEncoder, PopGenStatistics
)
```
### Load Genotype Data (VCF Example)
```python
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.
---
## 🧪 Development Notes
To run unit all tests:
```bash
pip install snpio[dev]
pytest tests/
```
---
## 🧾 License and Citation
SNPio is licensed under the [GPL-3.0 License](https://github.com/btmartin721/SNPio/blob/master/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.
---
## 🤝 Contributing
We welcome community contributions!
- Report bugs or request features on [GitHub Issues](https://github.com/btmartin721/snpio/issues)
- Submit a pull request
- See [CONTRIBUTING.md](https://github.com/btmartin721/SNPio/blob/master/CONTRIBUTING.md) for contributing guidelines.
---
## 🙏 Acknowledgments
Thanks for using SNPio. We hope it facilitates your population genomic research. Feel free to reach out with questions or feedback!
Raw data
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"description": "# SNPio: A Python API for Population Genomic Data I/O, Filtering, Analysis, and Encoding\n\n\n\n**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.\n\nSNPio Includes:\n\n- File I/O (VCFReader, PhylipReader, StructureReader, GenePopReader)\n- Genotype filtering (NRemover2)\n- Genotype encoding for AI & machine learning applications (GenotypeEncoder)\n- Population genetic statistics & Principal Component Analysis (PopGenStatistics)\n- Experimental: Phylogenetic tree parsing (TreeParser)\n\n---\n\n## \ud83d\udcd6 Full Documentation\n\nDetailed API usage, tutorials, and examples are available in the [Documentation](https://snpio.readthedocs.io/en/latest/)\n\n---\n\n## \ud83d\udd27 Installation\n\nYou can install SNPio using one of the following methods:\n\n### \u2705 Pip Installation\n\n```bash\npython3 -m venv snpio-env\nsource snpio-env/bin/activate\npip install snpio\n```\n\n### \u2705 Conda Installation\n\n```bash\nconda create -n snpio-env python=3.12\nconda activate snpio-env\nconda install -c btmartin721 snpio\n```\n\n### \ud83d\udc33 Docker\n\nTo run the Docker image interactively in a terminal, run the following commands:\n\n```bash\ndocker pull btmartin721/snpio:latest\ndocker run -it btmartin721/snpio:latest\n```\n\nIf you'd like to run SNPio in a jupyter notebook, instructions to do so in the docker container will be printed to the terminal. \n\n> **Note:** All three installation versions (pip, conda, docker) are actively maintained and kept up-to-date with CI/CD routines.\n\n> **Note:** SNPio supports Unix-based systems. Windows users should install via WSL.\n\n---\n\n## \ud83d\ude80 Getting Started\n\n### Import Modules\n\n```python\nfrom snpio import (\n NRemover2, VCFReader, PhylipReader, StructureReader,\n GenePopReader, GenotypeEncoder, PopGenStatistics\n)\n```\n\n### Load Genotype Data (VCF Example)\n\n```python\nvcf = \"snpio/example_data/vcf_files/phylogen_subset14K_sorted.vcf.gz\"\npopmap = \"snpio/example_data/popmaps/phylogen_nomx.popmap\"\n\ngd = VCFReader(\n filename=vcf,\n popmapfile=popmap,\n force_popmap=True,\n verbose=True,\n plot_format=\"png\",\n prefix=\"snpio_example\"\n)\n```\n\nYou can also specify `include_pops` and `exclude_pops` to control population-level filtering.\n\n---\n\n## \ud83e\uddea Development Notes\n\nTo run unit all tests:\n\n```bash\npip install snpio[dev]\npytest tests/\n```\n\n---\n\n## \ud83e\uddfe License and Citation\n\nSNPio is licensed under the [GPL-3.0 License](https://github.com/btmartin721/SNPio/blob/master/LICENSE). \n\nPlease cite any publication(s) when using SNPio in your research. A manuscript is currently in development, and this section will be updated upon acceptance.\n\n---\n\n## \ud83e\udd1d Contributing\n\nWe welcome community contributions!\n\n- Report bugs or request features on [GitHub Issues](https://github.com/btmartin721/snpio/issues)\n- Submit a pull request\n- See [CONTRIBUTING.md](https://github.com/btmartin721/SNPio/blob/master/CONTRIBUTING.md) for contributing guidelines.\n\n---\n\n## \ud83d\ude4f Acknowledgments\n\nThanks for using SNPio. We hope it facilitates your population genomic research. Feel free to reach out with questions or feedback!\n",
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