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Parsing GTF and FASTA files using the eccLib Library
Tomasz Chady1, Zuzanna Karolina Filutowska2
1Department of Mathematical Statistics and Data Analysis, Faculty of Mathematics and Computer Science, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 4, Poznań, 61-614, Poland.
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 utilize 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 optimizations at both the implementation and algorithmic levels, which are either unachievable or impractical in Python.
