PxBLAT: An Ergonomic and Efficient Python Binding Library for BLAT

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 3.9+), and pre-compiled packages are released via PyPI (https://pypi.org/project/pxblat/) and Bioconda (https://anaconda.org/bioconda/pxblat). The source code and executables are freely available for academic, nonprofit and personal use. Commercial licensing information is available on the Kent Informatics website (http://www.kentinformatics.com). Its documentation is available on ReadTheDocs (https://pxblat.readthedocs.io/en/latest/).