GFFUtils: utilities for handling GFF and GTF files


The GFFUtils package provides a small set of utility programs for working with GFF and GTF files, specifically:

  • gff_cleaner: perform “cleaning” operations on a GFF file
  • gff_annotation_extractor: combine and annotate feature counts (e.g. from htseq-count) with data from a GFF file
  • gtf_extract: extract selected data items from a GTF file
  • gtf2bed: convert GTF file to BED format


The old names for the utilities (GFFcleaner, GFF3_Annotation_Extractor and GTF_extract) are still supported, but will be removed in a future release.


To install the latest version of GFFUtils, download the latest release from as a tar.gz file from:

For example for version 0.10.3, download GFFUtils-0.10.3.tar.gz.

Unpack the code using:

tar xzf GFFUtils-0.10.3.tar.gz

which will unpack into a new directory called e.g. GFFUtils-0.10.3.

It is recommended to install the code into a Python virtual environment, which you can create by doing:

virtualenv venv
source venv/bin/activate
pip install -r ./GFFUtils-0.10.3/requirements.txt
pip install ./GFFUtils-0.10.3/

To install the developmental code directly from GitHub:

pip install -r
pip install git+


GFFUtils is currently supported under the following Python versions:

  • 2.7
  • 3.5
  • 3.6
  • 3.7
  • 3.8

but support for Python 2.7 is likely to be dropped in the near future.

Version history


Additional information

See for details of the GFF format.


These utilities have been developed by Peter Briggs with input from Leo Zeef, to support the activities of the Bioinformatics Core Facility (BCF) in the Faculty of Biology Medicine and Health (FBMH) at the University of Manchester (UoM).