PyRanges: efficient comparison of genomic intervals in Python
PyRanges: efficient comparison of genomic intervals in Python
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DOI：
10.1093/bioinformatics/btz615
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发表时间：
2020-02-01
期刊：
影响因子：
5.8
通讯作者：
Saetrom, Pal
中科院分区：
文献类型：
--
作者：
Stovner, Endre Bakken;Saetrom, Pal
摘要：复杂的基因组分析通常使用简单的集合操作序列，如交叉，重叠和基因组间隔上的最近。这些操作，加上一些自定义编程，允许进行广泛的分析。为此，我们编写了PyRanges，这是一种用于在Python中表示和操作基因组间隔及其相关数据的数据结构。在二进制集合操作上运行单线程，PyRanges比流行的R GenomicRanges库快2.3-9.6倍，并且同样具有内存效率;在8个核心上运行多线程，我们的库快123倍。因此，PyRanges非常适合单独分析，并作为Python中未来基因组库的基础。
A 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.