🚀 Performance
Benchmarking
polars-bio significantly outperforms other libraries in terms of speed and memory usage. It was benchmarked against following libraries:
- Bioframe-0.7.2
- PyRanges-0.0.132
- pybedtools-0.10.0
- PyGenomics-0.1.1
- GenomicRanges-0.4.34
Todo
- Add more details about the benchmarking process.
- GenomicRanges
Test datasets
AIList dataset was used for benchmarking.
| Dataset# | Name(.bed) | size(x1000) | non-flatness |
|---|---|---|---|
| 0 | chainRn4 | 2,351 | 6 |
| 1 | fBrain | 199 | 1 |
| 2 | exons | 439 | 2 |
| 3 | chainOrnAna1 | 1,957 | 6 |
| 4 | chainVicPac2 | 7,684 | 8 |
| 5 | chainXenTro3Link | 50,981 | 7 |
| 6 | chainMonDom5Link | 128,187 | 7 |
| 7 | ex-anno | 1,194 | 2 |
| 8 | ex-rna | 9,945 | 7 |
Note
Test dataset in Parquet format can be downloaded from:
- for single-threaded tests
- for parallel tests (8 partitions per dataset)
Results
Overlap operation
Nearest interval operation
