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
To install from github, do:
pip2 install -r https://raw.githubusercontent.com/fls-bioinformatics-core/GFFUtils/master/requirements.txt
pip2 install git+https://github.com/fls-bioinformatics-core/GFFUtils.git
Note
GFFUtils
requires Python 2 and doesn't currently work with Python 3.
install GFFcleaner GFF3_Annotation_Extractor GTF_extract gtf2bed extras
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 Life Sciences (FLS) at the University of Manchester (UoM).
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