polars-bio

# polars-bio ## Overview polars-bio is a high-performance Python library for genomic interval operations and bioinformatics file I/O, built on Polars, Apache Arrow, and Apache DataFusion. It provides a familiar DataFrame-centric API for interval arithmetic (overlap, nearest, merge, coverage, complement, subtract) and reading/writing common bioinformatics formats (BED, VCF, BAM, CRAM, GFF/GTF, FASTA, FASTQ). Key value propositions: - **6-38x faster** than bioframe on real-world genomic benchmarks - **Streaming/out-of-core** support for large genomes via DataFusion - **Cloud-native** file I/O (S3, GCS, Azure) with predicate pushdown - **Two API styles**: functional (`pb.overlap(df1, df2)`) and method-chaining (`df1.lazy().pb.overlap(df2)`) - **SQL interface** for genomic data via DataFusion SQL engine ## When to Use This Skill Use this skill when: - Performing genomic interval operations (overlap, nearest, merge, coverage, complement, subtract) - Reading/writing bioinformatics file formats (BED, VCF, BAM, CRAM, GFF/GTF, FASTA, FASTQ) - Processing large genomic datasets that don't fit in memory (streaming mode) - Running SQL queries on genomic data files - Migrating from bioframe to a faster alternative - Computing read depth/pileup from BAM/CRAM files - Working with Polars DataFrames containing genomic intervals ## Quick Start ### Installation ```bash pip install polars-bio # or uv pip install polars-bio ``` For pandas compatibility: ```bash pip install polars-bio[pand...