sangerpathogens/gff3toembl repository overview

⁠GFF3toEMBL

Converts GFF3 files from Prokka into a format suitable for submission to EMBL.

⁠Contents

• Introduction⁠
• Installation⁠
  • Required dependencies⁠
  • Docker⁠
  • From source⁠
  • Running the tests⁠
• Usage⁠
  • Example data⁠
• License⁠
• Feedback/Issues⁠
• Citation⁠
• Known Issues⁠

⁠Introduction

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.

N.B. This implements some EMBL specific conventions and is not a generic conversion tool. It is also not a validator, so you need to pass in parameters which are acceptable to EMBL.

⁠Installation

GFF3toEMBL has the following dependencies:

⁠Required dependencies

• Genometools⁠

There are a number of ways to install GFF3toEMBL and details are provided below. If you encounter an issue when installing GFF3toEMBL please contact your local system administrator. If you encounter a bug please log it here⁠ or email us at [email protected]⁠.

⁠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 sangerpathogens/gff3toembl gff3_to_embl --output_filename /data/output_file.embl ABC 123 PRJ1234 ABC /opt/gff3toembl-1.1.0/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

⁠Running the tests

Run python setup.py test

⁠Usage

usage: gff3_to_embl [-h] [--authors AUTHORS] [--title TITLE]
                    [--publication PUBLICATION] [--genome_type GENOME_TYPE]
                    [--classification CLASSIFICATION]
                    [--output_filename OUTPUT_FILENAME]
                    [--locus_tag LOCUS_TAG]
                    [--translation_table TRANSLATION_TABLE]
                    [--chromosome_list CHROMOSOME_LIST] [--version]
                    organism taxonid project_accession description file

Converts prokaryote GFF3 annotations to EMBL for ENA submission. Cite
http://dx.doi.org/10.21105/joss.00080

positional arguments:
  organism              Organism
  taxonid               Taxon id
  project_accession     Accession number for the project
  description           Genus species subspecies strain of organism
  file                  GFF3 filename

optional arguments:
  -h, --help            show this help message and exit
  --authors AUTHORS, -i AUTHORS
                        Authors (in the EMBL RA line style)
  --title TITLE, -m TITLE
                        Title of paper (in the EMBL RT line style)
  --publication PUBLICATION, -p PUBLICATION
                        Publication or journal name (in the EMBL RL line
                        style)
  --genome_type GENOME_TYPE, -g GENOME_TYPE
                        Genome type (linear/circular)
  --classification CLASSIFICATION, -c CLASSIFICATION
                        Classification (PROK/UNC/..)
  --output_filename OUTPUT_FILENAME, -f OUTPUT_FILENAME
                        Output filename
  --locus_tag LOCUS_TAG, -l LOCUS_TAG
                        Overwrite the locus tag in the annotation file
  --translation_table TRANSLATION_TABLE, -n TRANSLATION_TABLE
                        Translation table
  --chromosome_list CHROMOSOME_LIST, -d CHROMOSOME_LIST
                        Create a chromosome list file, and use the supplied
                        name
  --version             show program's version number and exit

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.

⁠License

GFF3toEMBL is free software, licensed under GPLv3⁠.

⁠Feedback/Issues

Please report any issues to the issues page⁠ or email [email protected]⁠.

⁠Citation

If you use this software please cite:

GFF3toEMBL: Preparing annotated assemblies for submission to EMBL
Andrew J. Page, Sascha Steinbiss, Ben Taylor, Torsten Seemann, Jacqueline A. Keane
The Journal of Open Source Software, 1 (6) 2016. doi: 10.21105/joss.00080⁠

⁠Known Issues

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