polars-bio

Python library polars-bio for genomic interval operations and bioinformatics file I/O on Polars DataFrames, built on Arrow and DataFusion. Covers overlap, nearest, merge, cluster, coverage, complement, subtract, count_overlaps, per-base pileup depth, and read/scan/write of BED, VCF, BAM, CRAM, SAM, GFF/GTF, FASTA, FASTQ, plus SQL queries over those files. Use when intersecting or merging genomic intervals in Polars. Use when reading or streaming large BED, VCF, or BAM files, including from S3, GCS, or Azure. Use when computing read depth from BAM or CRAM. Use when running SQL on genomic files. Use when migrating bioframe code to a faster alternative. Not for pandas-only workflows that do not use Polars or DataFusion.

Version

1.1

License

Apache-2.0

Compatibility

Requires Python 3.11–3.14 and polars-bio (uv pip install). Cloud I/O uses standard AWS/GCS/Azure SDK env vars when paths use s3://, gs://, or az:// URIs.