PyRanges: efficient comparison of genomic intervals in Python

Abstract

Summary: Complex genomic analyses often use sequences of simple set operations like intersection, overlap and nearest on genomic intervals. These operations, coupled with some custom programming, allow a wide range of analyses to be performed. To this end, we have written PyRanges, a data structure for representing and manipulating genomic intervals and their associated data in Python. Run single threaded on binary set operations, PyRanges is in median 2.3-9.6 times faster than the popular R GenomicRanges library and is equally memory efficient; run multi-threaded on 8 cores, our library is up to 123 times faster. PyRanges is therefore ideally suited both for individual analyses and as a foundation for future genomic libraries in Python.

Availability and implementation: PyRanges is available as open source under the MIT license at https://github.com/biocore-NTNU/pyranges and the documentation exists at https://biocore-NTNU.github.io/pyranges/.

Supplementary information: Supplementary data are available at Bioinformatics online.