Parsing GTF and FASTA files using the eccLib Library
Year: 2025
Type: article
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 [email protected] , [email protected] , [email protected] 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 . More detailed documentation can be accessed at https://gitlab-pages.platinum.edu.pl/eccdna/eccLib/ .
Source: Bioinformatics
Authors: Tomasz Chady, Zuzanna Karolina Filutowska
Institution: Adam Mickiewicz University in Poznań
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,989
OpenAlex ID: W4414903669