polars_bio

Features

Genomic ranges operations

Features	Bioframe	polars-bio	PyRanges	Pybedtools	PyGenomics	GenomicRanges
overlap	✅	✅	✅	✅	✅	✅
nearest	✅	✅	✅
cluster	✅
merge	✅
complement	✅
select/slice	✅
coverage	✅
expand	✅
sort	✅

Input/Output

I/O	Bioframe	polars-bio	PyRanges	Pybedtools	PyGenomics	GenomicRanges
Pandas DataFrame	✅	✅	✅
Polars DataFrame		✅
Polars LazyFrame		✅
Native readers		✅

Genomic file format

I/O	Bioframe	polars-bio	PyRanges	Pybedtools	PyGenomics	GenomicRanges
BED	✅		✅
BAM
VCF

Performance

Remarks

Pyranges is multithreaded, but :

• Requires Ray backend plus

  nb_cpu: int, default 1

            How many cpus to use. Can at most use 1 per chromosome or chromosome/strand tuple.
            Will only lead to speedups on large datasets.

• for nearest returns no empty rows if there is no overlap (we follow Bioframe where nulls are returned)