Execute genomic interval operations on Polars DataFrames and LazyFrames.
npx skills add https://github.com/gabrielvuksani/wotann --skill polars-bio-gabrielvuksani
Please help me install this Agent Skill. Skill: polars-bio Source: https://github.com/gabrielvuksani/wotann/tree/main/skills/scientific/polars-bio Command: npx skills add https://github.com/gabrielvuksani/wotann --skill polars-bio-gabrielvuksani
This Skill solves slow, memory-heavy genomic interval computations by providing high-performance overlap, nearest, merge, coverage, complement, and subtract operations directly on Polars DataFrames.
Use the polars-bio skill to compute streaming overlaps between two BED files named 'regions.bed' and 'genes.bed' and return the result as a Polars DataFrame.
High-intent search queries and answers about installing and using this skill.
Genomic interval overlaps on BED files are computed directly on Polars DataFrames by returning LazyFrames for scalable, memory-efficient streaming execution before materializing with .collect().
Nearest, merge, coverage, complement, and subtract operations are executed as high-performance genomic interval arithmetic on Polars DataFrames using DataFusion-backed interval logic.
You can register bioinformatics files like VCF and BAM as SQL tables using DataFusion SQL integration, query them with standard SQL, and subsequently run interval operations on the results.
Streaming scans are supported for large bioinformatics file formats including BED, VCF, BAM/CRAM, GFF/GTF, FASTA/FASTQ, SAM, and Hi-C pairs to handle memory-heavy genomic datasets efficiently.
Pileup depth is calculated directly from BAM and CRAM files within the Polars pipeline, integrating bioinformatics file I/O with genomic interval analytics for downstream processing.
Correct coordinate-system handling is managed via metadata during DataFusion-backed interval arithmetic, ensuring accurate overlap and coverage results across BED and GFF formats.
dralkhCompute genomic interval overlaps, merges, and coverage on Polars DataFrames.
AlterLab-IEURead, process, and write genomic data in SAM/BAM/CRAM, VCF/BCF, and FASTA/FASTQ formats.
shushuznPerform genomic interval operations and bioinformatics file I/O in Polars DataFrames.
LogauaEngstromAnalyze genomic intervals with Rust-based overlap detection and coverage track generation.
