GFFUtils: utilities for handling GFF and GTF files¶
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 (
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
Unpack the code using:
tar xzf GFFUtils-0.10.3.tar.gz
which will unpack into a new directory called e.g.
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 https://raw.githubusercontent.com/fls-bioinformatics-core/GFFUtils/devel/requirements.txt pip install git+https://github.com/fls-bioinformatics-core/GFFUtils.git@devel
GFFUtils is currently supported under the following Python
but support for Python 2.7 is likely to be dropped in the near future.
gff_cleaner: clean up GFF files
gff_annotation_extractor: annotate gene feature data
gtf_extract: extract data items from GTF/GFF
gtf2bed: convert GTF contents to BED format
- Extra scripts and utilities
See http://www.sanger.ac.uk/resources/software/gff/spec.html 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).