Parsing GTF

We have provided several utility scripts to parse GTF files into tab-delimited files, which allows users to easily use table operations (e.g., working as dataframes in R or pandas in Python) to manipulate the data.

The scripts will extract either the gene, transcript, or exon information from the GTF file.

• Gene information: extract_gene_from_gtf.py
• Transcript information: extract_transcript_from_gtf.py
• Exon information: extract_exon_from_gtf.py

To make use of the scripts, users can run the following command:

python3 extract_gene_from_gtf.py <path_to_gtf_file> <output_file>

The output file will be a tab-delimited file containing gene/transcript/exon attributes.