Parsing GTF and FASTA files using the eccLib Library.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41056409.
- Also identified by DOI 10.1093/bioinformatics/btaf558 and PMC identifier 12552103.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
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. 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.
Medical subject headings
- Software
- Genomics