Li Yangyang, Yang Rendong
Department of Urology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
bioRxiv. 2024 Feb 5:2023.08.02.551686. doi: 10.1101/2023.08.02.551686.
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. Moreover, PxBLAT's design philosophy emphasizes ease of use, memory efficiency, and the elimination of intermediary files and unnecessary system calls, thereby enhancing computational speed and user experience. Benchmark tests reveal its superior performance across various datasets, illustrating its capacity to maintain correctness. PxBLAT supports Python (version 3.9+), and pre-compiled packages are released via PyPI (https://pypi.org/project/pxblat/) and Bioconda (https://anaconda.org/bioconda/pxblat). The source code and executable are freely available for academic, nonprofit, and personal use. Its documentation is available on ReadTheDocs (https://pxblat.readthedocs.io/en/latest/).
我们介绍了PxBLAT，这是一个Python库，旨在提高与类BLAST比对工具（BLAT）交互时的可用性和效率。PxBLAT提供了直观的应用程序编程接口（API）设计，允许将其功能直接整合到基于Python的生物信息学工作流程中。此外，PxBLAT的设计理念强调易用性、内存效率以及消除中间文件和不必要的系统调用，从而提高计算速度和用户体验。基准测试表明，它在各种数据集上都具有卓越的性能，证明了其保持正确性的能力。PxBLAT支持Python（3.9+版本），预编译包通过PyPI（https://pypi.org/project/pxblat/）和Bioconda（https://anaconda.org/bioconda/pxblat）发布。源代码和可执行文件可供学术、非营利和个人使用。其文档可在ReadTheDocs（https://pxblat.readthedocs.io/en/latest/）上获取。
