Parsing GTF and FASTA files using the eccLib Library.

IF 5.4

Bioinformatics (Oxford, England) Pub Date : 2025-10-07 DOI:10.1093/bioinformatics/btaf558

Tomasz Chady, Zuzanna Karolina Filutowska

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Abstract

Summary: Leveraging the Python/C API, eccLib was developed as a high-performance library designed for parsing genomic files and analysing genomic contexts. To the best of the authors' knowledge, it is the fastest Python-based solution available. With eccLib, users can efficiently parse GTF/GFFv3 and FASTA files and utilise the provided methods for additional analysis.

Availability and implementation: This library is implemented in C and distributed under the GPL-3.0 licence. It is compatible with any system that has the Python interpreter (CPython) installed. The use of C enables numerous optimisations at both the implementation and algorithmic levels, which are either unachievable or impractical in Python.

Contact: tomcha@st.amu.edu.pl, platyna@amu.edu.pl, eccdna@eccdna.pl.

Supplementary information: This library is available for installation from the Python Package Index (PyPI) under the name eccLib https://pypi.org/project/eccLib/. The source code is available at https://gitlab.platinum.edu.pl/eccdna/eccLib. The version described by this document (1.1.0) is archived as https://doi.org/10.5281/zenodo.17024282. More detailed documentation can be accessed at https://gitlab-pages.platinum.edu.pl/eccdna/eccLib/.

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使用eccLib库解析GTF和FASTA文件。

eccLib是利用Python/C API开发的高性能库，用于解析基因组文件和分析基因组上下文。据作者所知，它是最快的基于python的解决方案。使用eccLib，用户可以有效地解析GTF/GFFv3和FASTA文件，并利用提供的方法进行额外的分析。可用性和实现：这个库是用C语言实现的，并在GPL-3.0许可下发布。它与安装了Python解释器（CPython）的任何系统兼容。使用C可以在实现和算法级别进行大量优化，这些优化在Python中要么无法实现，要么不切实际。联系：tomcha@st.amu.edu.pl, platyna@amu.edu.pl, eccdna@eccdna.pl.Supplementary信息：该库可从Python包索引（PyPI）中安装，名称为eccLib https://pypi.org/project/eccLib/。源代码可从https://gitlab.platinum.edu.pl/eccdna/eccLib获得。本文档描述的版本号为1.1.0，存档号为https://doi.org/10.5281/zenodo.17024282。更详细的文档可以访问https://gitlab-pages.platinum.edu.pl/eccdna/eccLib/。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Bioinformatics (Oxford, England)

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