GFFUtils: utilities for handling GFF and GTF files¶
Overview¶
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 filegff_annotation_extractor
: combine and annotate feature counts (e.g. fromhtseq-count
) with data from a GFF filegtf_extract
: extract selected data items from a GTF filegtf2bed
: convert GTF file to BED format
Warning
The old names for the utilities (GFFcleaner
,
GFF3_Annotation_Extractor
and GTF_extract
) are
still supported, but will be removed in a future release.
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
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.
Contents¶
Additional information¶
See http://www.sanger.ac.uk/resources/software/gff/spec.html for details of the GFF format.
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).