RT Journal Article
SR Electronic
T1 PyRanges: efficient comparison of genomic intervals in Python
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 609396
DO 10.1101/609396
A1 Endre Bakken Stovner
A1 Pål Sætrom
YR 2019
UL http://biorxiv.org/content/early/2019/04/16/609396.abstract
AB 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 PyRanges is available open-source under the MIT license at https://github.com/biocore-NTNU/pyranges and documentation exists at https://biocore-NTNU.github.io/pyranges/Contact endrebak85{at}gmail.comSupplementary information Supplementary data are available.