pxblat 0.3.6

A native python binding for blat suit

PxBLAT

An Efficient and Ergonomic Python Binding Library for BLAT

Why PxBLAT?

When conducting extensive queries, using the blat of BLAT suit can prove to be quite inefficient, especially if these operations aren't grouped. The tasks are allocated sporadically, often interspersed among other tasks. In general, the choice narrows down to either utilizing blat or combining gfServer with gfClient. Indeed, blat is a program that launches gfServer, conducts the sequence query via gfClient, and then proceeds to terminate the server.

This approach is far from ideal when performing numerous queries that aren't grouped since blat repeatedly initializes and shuts down gfServer for each query, resulting in substantial overhead. This overhead consists of the time required for the server to index the reference, contingent on the reference's size. To index the human genome (hg38), for example, would take approximately five minutes.

A more efficient solution would involve initializing gfServer once and invoking gfClient multiple times for the queries. However, gfServer and gfClient are only accessible via the command line. This necessitates managing system calls (for instance, subprocess or os.system), intermediate temporary files, and format conversion, further diminishing performance.

That is why PxBLAT holds its position. It resolves the issues mentioned above while introducing handy features like port retry, use current running server, etc.

📚 Table of Contents

• PxBLAT
  • 📚 Table of Contents
  • 🔮 Features
  • 📎 Citation
  • 🚀 Getting Started
  • 🤝 Contributing
  • 🪪 License
  • Contributors
  • 🙏 Acknowledgments

🔮 Features

• Zero System Calls: Avoids system calls, leading to a smoother, quicker operation.
  
• Ergonomics: With an ergonomic design, PxBLAT aims for a seamless user experience.
  
• No External Dependencies: PxBLAT operates independently without any external dependencies.
  
• Self-Monitoring: No need to trawl through log files; PxBLAT monitors its status internally.
  
• Robust Validation: Extensively tested to ensure reliable performance and superior stability as BLAT.
  
• Format-Agnostic: PxBLAT doesn't require you to worry about file formats.
  
• In-Memory Processing: PxBLAT discards the need for intermediate files by doing all its operations in memory, ensuring speed and efficiency.
  

📎 Citation

PxBLAT is scientific software, with a published paper in the BioRxiv. Check the published to read the paper.

@article {Li2023pxblat,
	author = {Yangyang Li and Rendong Yang},
	title = {PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT},
	elocation-id = {2023.08.02.551686},
	year = {2023},
	doi = {10.1101/2023.08.02.551686},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Summary: We introduce PxBLAT, a Python library designed to enhance usability and efficiency in interacting with the BLAST-like alignment tool (BLAT). PxBLAT provides an intuitive application programming interface (API) design, allowing the incorporation of its functionality directly into Python-based bioinformatics workflows. Besides, it integrates seamlessly with Biopython and comes equipped with user-centric features like server readiness checks and port retry mechanisms. PxBLAT removes the necessity for system calls and intermediate files, as well as reducing latency and data conversion overhead. Benchmark tests reveal PxBLAT gains a ~20\% performance boost compared to BLAT in the Python environment. Availability and Implementation: PxBLAT supports Python (version 3.8+), and pre-compiled packages are released via PyPI (https://pypi.org/project/ pxblat/) and Bioconda (https://anaconda.org/ bioconda/pxblat). The source code of PxBLAT is available under the terms of an open-source MIT license and hosted on GitHub (https:// github.com/ylab-hi/pxblat). Its documentation is available on ReadTheDocs (https://pxblat. readthedocs.io/en/latest/).Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2023/08/05/2023.08.02.551686},
	eprint = {https://www.biorxiv.org/content/early/2023/08/05/2023.08.02.551686.full.pdf},
	journal = {bioRxiv}
}

🚀 Getting Started

Please see the document for details and more examples.

🤝 Contributing

Contributions are always welcome! Please follow these steps:

1. Fork the project repository. This creates a copy of the project on your account that you can modify without affecting the original project.
2. Clone the forked repository to your local machine using a Git client like Git or GitHub Desktop.
3. Create a new branch with a descriptive name (e.g., new-feature-branch or bugfix-issue-123).

git checkout -b new-feature-branch

4. Take changes to the project's codebase.
5. Install the latest package

poetry install

6. Test your changes

pytest -vlsx tests

7. Commit your changes to your local branch with a clear commit message that explains the changes you've made.

git commit -m 'Implemented new feature.'

8. Push your changes to your forked repository on GitHub using the following command

git push origin new-feature-branch

Create a pull request to the original repository. Open a new pull request to the original project repository. In the pull request, describe the changes you've made and why they're necessary. The project maintainers will review your changes and provide feedback or merge them into the main branch.

🪪 License

PxBLAT is modified from blat, the license is the same as blat. The source code and executables are freely available for academic, nonprofit, and personal use. Commercial licensing information is available on the Kent Informatics website (https://kentinformatics.com/).

Contributors

yangliz5 🚧

Joshua Zhuang 🚇

🙏 Acknowledgments

• BLAT
• UCSC
• pybind11