PyRanges: efficient comparison of genomic intervals in Python.

Autor:	Stovner EB; Department of Computer Science, Trondheim 7013, Norway.; Department of Clinical and Molecular Medicine, Trondheim 7013, Norway.; Bioinformatics Core Facility, Trondheim 7013, Norway.; Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim 7013, Norway., Sætrom P; Department of Computer Science, Trondheim 7013, Norway.; Department of Clinical and Molecular Medicine, Trondheim 7013, Norway.; Bioinformatics Core Facility, Trondheim 7013, Norway.; Department of Public Health and Nursing, K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, Trondheim 7013, Norway.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2020 Feb 01; Vol. 36 (3), pp. 918-919.
DOI:	10.1093/bioinformatics/btz615
Abstrakt:	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. (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu