gff-to-genbank

Convert GFF file to GenBank file format while extracting the sequences between the annotated regions

Original script written by Brad Chapman and Hsiao Yi - https://github.com/chapmanb/bcbb/blob/master/gff/Scripts/gff/gff_to_genbank.py

Edited by Kartik Chundru to crop the FASTA sequence between the first and last annotated regions.

Edited by Cornelius Roemer to make it work with BioPython 1.81 and to allow compound CDS features. Made pip installable at https://pypi.org/project/gff-to-genbank/

Usage

Installation:

pip install gff-to-genbank

gff-to-genbank <gff_file> <fasta_file>

Output is written to stdout, so you'll want to redirect it to a file.

Dependencies

• BioPython - https://biopython.org/
• BCBio - https://github.com/chapmanb/bcbb

Development

Set new version:

hatch version <new_version>

Publishing to PyPi:

hatch build
hatch publish -u=__token__