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polars-bio Genomic Intervals

Run genomic interval joins, coverage and file I/O on Polars DataFrames with coordinate checks

Source Download skill
Repository
K-Dense-AI/scientific-agent-skills
Stars
55,780
Licence
MIT
Files
7 files

What it does

This skill teaches an AI agent how to work with genomic coordinate data (regions of DNA such as genes or sequencing reads) using the polars-bio Python library. Once installed, the agent can find overlapping or nearest genomic intervals, merge or subtract regions, compute coverage, and read or write common bioinformatics files such as BED, VCF, BAM and FASTQ. It also warns about coordinate-convention pitfalls, such as 1-based versus 0-based positions, and suggests checking results against small hand-computed examples.

Great for

  • Bioinformatics analysts who already use Polars and need coordinate-aware joins on genomic intervals
  • Researchers porting bioframe code to a faster Polars-based workflow
  • Developers building pipelines that read or convert BED, VCF, BAM or FASTQ files lazily

Skip it if

  • Users who do not work with genomic data, since the operations are specific to genomic intervals
  • Clinical or diagnostic decisions based on its output without independent validation, because boundary and coordinate conventions can silently change counts
  • Very large genomes or concatenated coordinate spaces above the 2,147,483,647 bound of the default overlap index, which can produce wrong results without validation

Try asking

  • “Find which of my BED peaks overlap genes in this GTF file and count hits per peak”
  • “Compute how many bases of my target regions are covered by these read intervals”
  • “Convert this bioframe merge script to polars-bio and check boundary behaviour”
  • “Read this BAM file lazily, filter by region, and save the result as a Parquet file”
Step-by-step guide: how to use polars-bio Genomic IntervalsInstall, first run, examples, tips and FAQs

Install in 3 steps

  1. 1

    Download the skill

    The ZIP contains the 7 original files, the MIT licence and an attribution note.

    polars-bio.zip
  2. 2

    Add it to your agent

    Claude Code (all projects)

    mkdir -p ~/.claude/skills && unzip polars-bio.zip -d ~/.claude/skills/

    Claude Code / Agent SDK (this project only)

    mkdir -p .claude/skills && unzip polars-bio.zip -d .claude/skills/

    Claude apps (web/desktop): Settings → Capabilities → Skills → Upload skill, and choose the ZIP.

  3. 3

    Ask for the task

    No special command needed — the agent reads the skill's description and loads it when your request matches. Try one of the prompts above.

Get better results

  • State the assembly, contig naming and coordinate convention (0-based or 1-based) up front so the agent sets metadata correctly.
  • Ask the agent to run a small hand-computable test fixture before applying the operation to full data.
  • Install polars-bio in a separate virtual environment, since its Arrow and DataFusion versions can conflict with other packages.

What's inside

  • references/bioframe_migration.md
  • references/configuration.md
  • references/file_io.md
  • references/interval_operations.md
  • references/pileup_operations.md
  • references/sql_processing.md
  • SKILL.md

Redistributed unmodified from K-Dense-AI/scientific-agent-skills under the MIT licence. The assessment was drafted with AI from the skill's files on 2026-10-29. Skills can instruct your agent to run code — read SKILL.md and any scripts before installing.