Explore, edit and leverage genomic annotations using Python GTF toolkit

Fabrice Lopez (1) , Guillaume Charbonnier (1) , Yasmina Kermezli (1) , Mohamed Belhocine (2) , Quentin Ferré (1) , N Zweig (3) , M. Aribi (4) , Aitor Gonzalez (1) , Salvatore Spicuglia (1) , Denis Puthier (1)

1 TAGC - Theories and Approaches of Genomic Complexity
2 Molecular Biology and Genetics Laboratory, Dubai, United Arab Emirates
3 AMU - Aix Marseille Université
4 The Laboratory of Applied Molecular Biology and Immunology, Tlemcen University, Algeria

Motivation: While Python has become very popular in bioinformatics, a limited number of libraries exist for fast manipulation of gene coordinates in Ensembl GTF format. Results: We have developed the GTF toolkit Python package (pygtftk), which aims at providing easy and powerful manipulation of gene coordinates in GTF format. For optimal performances, the core engine of pygtftk is a C dynamic library (libgtftk) while the Python API provides usability and readability for developing scripts. Based on this Python package, we have developed the gtftk command line interface that contains 57 sub-commands (v0.9.10) to ease handling of GTF files. These commands may be used to (i) perform basic tasks (e.g. selections, insertions, updates or deletions of features/keys), (ii) select genes/transcripts based on various criteria (e.g. size, exon number, TSS location, intron length, GO terms) or (iii) carry out more advanced operations such as coverage analyses of genomic features using bigWig files to create faceted read-coverage diagrams. In conclusion, the pygtftk package greatly simplifies the annotation of GTF files with external information while providing advance tools to perform gene analyses.

Domaines: Sciences du Vivant [q-bio]; Bio-informatique [q-bio.QM]

Fabrice Lopez, Guillaume Charbonnier, Yasmina Kermezli, Mohamed Belhocine, Quentin Ferré, et al.. Explore, edit and leverage genomic annotations using Python GTF toolkit. Bioinformatics, 2019, ⟨10.1093/bioinformatics/btz116⟩. ⟨hal-02078147⟩