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gff3toembl

Submitting annoated genomes to EMBL is a very difficult and time consuming process. This software converts GFF3 files from the most commonly use prokaryote annotation tool PROKKA into a format that is suitable for submission to EMBL. It has been used to prepare more than 30% of all annotated genomes in EMBL/GenBank.

Build Status

NB this implements some EMBL specific conventions and is not a generic conversion tool. Its also not a validator, so you need to pass in parameters which are acceptable to EMBL.

Installation

Docker

A docker container is provided with all of the dependancies setup and installed. To install the container:

docker pull sangerpathogens/gff3toembl

To run the script from within the container on test data (substituting /home/ubuntu/data for your own directory): docker run --rm -it -v /home/ubuntu/data:/data e7c9895ac6e5 gff3_to_embl --output_filename /data/output_file.embl ABC 123 PRJ1234 ABC /opt/gff3toembl-1.0.9/gff3toembl/tests/data/single_feature.gff

From source

This is for advanced users. The homebrew recipe, Dockerfile and the TravisCI install dependancies script all contain steps to setup depenancies and install the software so might be worth looking at for hints.

  • Install genometools including python bindings
  • git clone [email protected]:sanger-pathogens/gff3toembl.git
  • python setup.py install

Homebrew

gff3toembl only works with Python 2.7 and there are known issues on other versions of Python.If you are using OSX:

If you are using Linux:

  • Install http://linuxbrew.sh/
  • brew tap homebrew/science
  • brew tap tseemann/homebrew-bioinformatics-linux
  • brew install gff3toembl

Example usage

Run the following to get usage: gff3_to_embl -h

An example:

gff3_to_embl --authors 'John' --title 'Some title' --publication 'Some journal' \
             --genome_type 'circular' --classification 'PROK' \
             --output_filename /tmp/single_feature.embl --translation_table 11 \
             Organism 1234 'My project' 'My description' gff3toembl/tests/data/single_feature.gff

Example data

The directory 'example_data' contains an input GFF file and the output file along with the command.

Tests

Run python setup.py test

Known Issues

This doesn't work with some versions of Genometools on Mac OS X; it appears to work with Genometools 1.5.4