Description
polars-bio is an agent skill for genomic interval arithmetic and bioinformatics file input and output, using Polars and DataFusion. It covers overlap, nearest-neighbour, merge, coverage, complement and subtraction operations on Polars DataFrames, and reading or writing BED, VCF, BCF, BAM and CRAM files. The skill targets polars-bio 0.36.0, tested with Polars 1.44.2 on Python 3.13. The upstream package requires Polars 1.37.1 or newer, PyArrow from 23.0.1 up to but not including 25, DataFusion from 53 up to but not including 54, and polars-config-meta from 0.3.2 up to but not including 1. The skill advises keeping this environment separate from packages that need incompatible Arrow or DataFusion releases. It recommends checking new releases against the official release notes and package requirements. The examples that name files are templates, so you must substitute your own files and check their schemas. The synthetic interval example and small local format round-trip tests were run during the review. A pandas-compatible option is available if you install pandas 3 or newer alongside it.…
Highlights
- Overlap, nearest, merge and coverage on intervals
- Complement and subtraction
- BED, VCF, BCF, BAM and CRAM input and output
- Works on Polars DataFrames
- Targets polars-bio 0.36.0
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polars-bio FAQ
What interval operations does it support?
Overlap, nearest, merge, coverage, complement and subtraction on genomic intervals in Polars DataFrames.
Which file formats?
BED, VCF, BCF, BAM and CRAM, for reading and writing.
Which versions were tested?
polars-bio 0.36.0 with Polars 1.44.2 on Python 3.13.
Why keep a separate environment?
The upstream package needs specific Arrow and DataFusion versions, which can conflict with other packages.
How do I install it?
Run npx skills add https://github.com/k-dense-ai/scientific-agent-skills --skill polars-bio.
Is it checked for security?
Its security audits show passes from Gen Agent Trust Hub, Socket and Snyk.
What are the best polars-bio alternatives?
Popular alternatives to polars-bio include geniml, gtars and gget. See all polars-bio alternatives