Generate GFF file from EMBL/Genbank

This tool makes it easy to get a .fa and .gff from given GenBank or EMBL files.

Why?

QUAST: Quality Assessment Tool for Genome Assemblies wants references and genes in FASTA format and GFF respectively. Most often our internal completed/closed strains are only available in GenBank or EMBL format.

Usage

Something like:

$ to-gff -h
usage: to-gff [-h] [-v] [--embl] [--getfasta] in_file out_file

to_gff v0.1 - Generate gff file from EMBL/Genbank for QUAST
(http://github.com/mscook/to_gff)

positional arguments:
  in_file        Full path to the input .embl/.gbk
  out_file       Full path to the output GFF

optional arguments:
  -h, --help     show this help message and exit
  -v, --verbose  verbose output
  --embl         Whether we have an EMBL or GenBank (default)
  --getfasta     Get a FASTA file (default = no)

Licence: ECL 2.0 by Mitchell Stanton-Cook <[email protected]>

Examples

Example usage:

# get data file
$ wget http://beatsonlab.com/static/downloads/EC958.chr.complete.embl

# get ~/EC958.gff
$ to-gff EC958.chr.complete.embl ec958.gff --embl

# get ~/EC958.gff & EC958.fa
$ rm ec958.gff
$ to-gff EC958.chr.complete.embl ec958.gff --embl --getfasta

Requirements

Requires following (thanks to the authors):

• bcbio-gff>=0.2
• biopython>=1.62b