Pygenomics：在 Python 中操作基因组区间和数据文件。

Pygenomics: manipulating genomic intervals and data files in Python.

机构信息

Institute for Translational Biomedicine, Saint Petersburg State University, St. Petersburg 199034, Russia.

出版信息

Bioinformatics. 2023 Jun 1;39(6). doi: 10.1093/bioinformatics/btad346.

DOI:10.1093/bioinformatics/btad346

PMID:37228014

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10246576/

Abstract

SUMMARY

We present pygenomics, a Python package for working with genomic intervals and bioinformatic data files. The package implements interval operations, provides both API and CLI, and supports reading and writing data in widely used bioinformatic formats, including BAM, BED, GFF3, and VCF. The source code of pygenomics is provided with in-source documentation and type annotations and adheres to the functional programming paradigm. These features facilitate seamless integration of pygenomics routines into scripts and pipelines. The package is implemented in pure Python using its standard library only and contains the property-based testing framework. Comparison of pygenomics with other Python bioinformatic packages with relation to features and performance is presented. The performance comparison covers operations with genomic intervals, read alignments, and genomic variants and demonstrates that pygenomics is suitable for computationally effective analysis.

AVAILABILITY AND IMPLEMENTATION

The source code is available at https://gitlab.com/gtamazian/pygenomics.

摘要

我们介绍了 pygenomics，这是一个用于处理基因组区间和生物信息学数据文件的 Python 包。该包实现了区间操作，提供了 API 和 CLI，并支持以广泛使用的生物信息学格式（包括 BAM、BED、GFF3 和 VCF）读写数据。pygenomics 的源代码提供了内联文档和类型注释，并遵循函数式编程范式。这些特性使得 pygenomics 例程能够无缝集成到脚本和管道中。该包完全使用 Python 标准库实现，仅包含基于属性的测试框架。我们展示了 pygenomics 与其他 Python 生物信息学包在功能和性能方面的比较。性能比较涵盖了基因组区间、读取对齐和基因组变异的操作，并证明了 pygenomics 适用于高效的计算分析。