GFFUtils

Utilities for working with GFF and GTF files:

• gff_cleaner.py: perform various "cleaning" manipulations on a GFF file
• gff_annotation_extractor: combine and annotate feature counts with data from a GFF or GTF file
• gft_extract: extract selected data items from a GTF file
• gtf2bed: convert GTF contents to BED format

Full documentation is available at http://gffutils.readthedocs.org/

Installation

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

https://github.com/fls-bioinformatics-core/GFFUtils/releases

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 https://raw.githubusercontent.com/fls-bioinformatics-core/GFFUtils/devel/requirements.txt
pip install git+https://github.com/fls-bioinformatics-core/GFFUtils.git@devel

Note that GFFUtils is currently supported for 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.

Licensing

This software is licensed under the Academic Free License 3.

Credits

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).