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:
GFFcleaner
: perform “cleaning” operations on a GFF fileGFF3_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
Installation¶
To install from github, do:
pip install -r https://raw.githubusercontent.com/fls-bioinformatics-core/GFFUtils/refactor/requirements.txt
pip install git+https://github.com/fls-bioinformatics-core/GFFUtils.git
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 Life Sciences (FLS) at the University of Manchester (UoM).