polars-bio—fast, scalable and out-of-core operations on large genomic interval datasets

Motivation Genomic studies very often rely on computationally intensive analyses of relationships between features, which are typically represented as intervals along a one-dimensional coordinate system (such as positions on a chromosome). In this context, the Python programming language is extensively used for manipulating and analyzing data stored in a tabular form of rows and columns, called a DataFrame. Pandas is the most widely used Python DataFrame package and has been criticized for inefficiencies and scalability issues, which its modern alternative—Polars—aims to address with a native backend written in the Rust programming language. Results polars-bio is a Python library that enables fast, parallel and out-of-core operations on large genomic interval datasets. Its main components are implemented in Rust, using the Apache DataFusion query engine and Apache Arrow for efficient data representation. It is compatible with Polars and Pandas DataFrame formats. In a real-world comparison (107 vs. 1.2×106 intervals), our library runs overlap queries 6.5x, nearest queries 15.5x, count_overlaps queries 38x, and coverage queries 15x faster than Bioframe. On equally-sized synthetic sets (107 vs. 107), the corresponding speedups are 1.6x, 5.5x, 6x, and 6x. In streaming mode, on real and synthetic interval pairs, our implementation uses 90x and 15x less memory for overlap, 4.5x and 6.5x less for nearest, 60x and 12x less for count_overlaps, and 34x and 7x less for coverage than Bioframe. Multi-threaded benchmarks show good scalability characteristics. To the best of our knowledge, polars-bio is the most efficient single-node library for genomic interval DataFrames in Python. Availability and implementation polars-bio is an open-source Python package distributed under the Apache License available for major platforms, including Linux, macOS, and Windows in the PyPI registry. The online documentation is https://biodatageeks.org/polars-bio/ and the source code is available on GitHub: https://github.com/biodatageeks/polars-bio and Zenodo: https://doi.org/10.5281/zenodo.16374290. Supplementary Materials are available at Bioinformatics online.