GfaPy：一个用于在 Python 中处理序列图的灵活可扩展的软件库。

GfaPy: a flexible and extensible software library for handling sequence graphs in Python.

机构信息

ZBH - Center for Bioinformatics, MIN-Fakultät, Universität Hamburg, 20146 Hamburg, Germany.

出版信息

Bioinformatics. 2017 Oct 1;33(19):3094-3095. doi: 10.1093/bioinformatics/btx398.

DOI:10.1093/bioinformatics/btx398

PMID:28645150

Abstract

SUMMARY

GFA 1 and GFA 2 are recently defined formats for representing sequence graphs, such as assembly, variation or splicing graphs. The formats are adopted by several software tools. Here, we present GfaPy, a software package for creating, parsing and editing GFA graphs using the programming language Python. GfaPy supports GFA 1 and GFA 2, using the same interface and allows for interconversion between both formats. The software package provides a simple interface for custom record types, which is an important new feature of GFA 2 (compared to GFA 1). This enables new applications of the format.

AVAILABILITY AND IMPLEMENTATION

GfaPy is available open source at https://github.com/ggonnella/gfapy and installable via pip.

CONTACT

gonnella@zbh.uni-hamburg.de.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

摘要

GFA 1 和 GFA 2 是最近定义的用于表示序列图（如组装、变异或剪接图）的格式。这些格式被几个软件工具采用。在这里，我们介绍了 GfaPy，这是一个使用编程语言 Python 创建、解析和编辑 GFA 图的软件包。GfaPy 支持 GFA 1 和 GFA 2，使用相同的接口，并允许在两种格式之间进行转换。该软件包提供了一个简单的接口，用于自定义记录类型，这是 GFA 2 （与 GFA 1 相比）的一个重要新特性。这使得该格式可以应用于新的领域。