#!/usr/bin/perl
# 
# This script assumes that the input GFF file has only CDS/tRNA/rRNA/tmRNA 
# features. It adds gene features to all of them, and also adds "mRNA" features
# to each CDSs.
#
#
while (<>) {
  chomp;
  print $_, "\n" if /^#/;
  last if /^##FASTA/ || /^>/;

  my @data = split /\t/, $_;
   
  if ($data[2] =~ /(CDS|rRNA|tRNA|tmRNA)/) {  # skip e.g. repeat_region
      $type = $1;
      $data[2] = 'gene';
      print join "\t", @data; print "\n";     # add gene feature
      
      if ($type eq 'CDS') {
          $data[2] = 'mRNA';
          print join "\t", @data; print "\n";
      }
  }
  print $_, "\n";   # print the original line 
}