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 file
• GFF3_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

Installation

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.

Contents

• GFFcleaner: clean up GFF files
  • Overview
  • Usage and options
  • Output files
  • Usage recipe
  • SGD grouping
  • Mapping file format
  • Overlap criteria
• GFF3_Annotation_Extractor: annotate gene feature data
  • Overview
  • Usage and options
  • Output files
• GTF_extract: extract data items from GTF/GFF
  • Overview
  • Usage and options
  • Output
• gtf2bed: convert GTF contents to BED format
  • Overview
  • Usage
  • Output
• Extra scripts and utilities
  • run_cleanup.sh

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).

Indices and tables

• Index
• Module Index
• Search Page