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bioRxiv · 10.1101/2025.04.24.650481

Parsing GTF and FASTA files using the eccLib Library

Chady, T.·Filutowska, Z. K.
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Abstract

SummaryLeveraging 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 ImplementationThis 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. Contacttomcha@st.amu.edu.pl, platyna@amu.edu.pl, eccdna@eccdna.pl Supplementary informationThis 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/.

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Chady, T., Filutowska, Z. K.. 2025-04-27. Parsing GTF and FASTA files using the eccLib Library. https://doi.org/10.1101/2025.04.24.650481

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