Converts PROKKA GFF3 files to EMBL files for uploading annotated assemblies to EBI.

NB this implements some EBI 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.

gff3toembl only works with Python 2.7 and there are known issues on other versions of Python.

• Install HomeBrew/LinuxBrew
• brew tap homebrew/science
• brew install https://raw.githubusercontent.com/andrewjpage/homebrew-science/gff3toembl/gff3toembl.rb

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

Run python setup.py test

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