Several scripts/command for converting output of gene prediction programs to variants of GFF3 compatible with ParsEval.

augustus-gff3-groom.sh

#!/usr/bin/env bash
# Usage: bash augustus-gff3-groom.sh genes-before.gff3 > genes-after.gff3

sed $'s/\ttranscript\t/\tmRNA\t/' < $1 | grep -v $'\tintron\t'

genemarkhmm3-gff3-groom.sh

#!/usr/bin/env bash
# Usage: bash genemarkhmm3-gff3-groom.sh genes-before.gff3 > genes-after.gff3

perl -ne 's/ID=cds(\d+)(.+)Parent=mRNA(\d+)/ID=cds$3$2Parent=mRNA$3/; print' < $1

glimmerhmm-gff3-groom.sh

#!/usr/bin/env bash
# Usage: bash glimmerhmm-gff3-groom.sh genes-before.gff3 > genes-after.gff3

perl -ne 'if(m/\tmRNA\t/){ $g = $_; $g =~ s/ID=([^;]+);/ID=$1.gene;/; $g =~ s/\tmRNA\t/\tgene\t/; print $g; $_ =~ s/ID=([^;]+)(\S+)/ID=$1$2;Parent=$1.gene/ } print' < $1

snap2gff3.pl

#!/usr/bin/env perl
# Usage: perl snap2.gff3 < genes-before.gff > genes-after.gff3
use strict;

my @exons;
sub by_position
{
  $a->[3] <=> $b->[3] or $a->[4] <=> $b->[4]
}

while(<STDIN>)
{
  chomp;
  my @v = split(/\t/);
  push(@exons, \@v);
  if($v[2] eq "Eterm" or $v[2] eq "Esngl")
  {
    @exons = sort by_position @exons;
    my $numexons = scalar(@exons);
    my $start = $exons[0]->[3];
    my $end = $exons[$numexons-1]->[4];
    printf
    (
      "%s\tSNAP\tgene\t%lu\t%lu\t.\t%s\t.\tID=%s.gene\n",
      $exons[0]->[0],
      $start,
      $end,
      $exons[0]->[6],
      $exons[0]->[8],
    );
    printf
    (
      "%s\tSNAP\tmRNA\t%lu\t%lu\t.\t%s\t.\tID=%s.mrna;Parent=%s.gene\n",
      $exons[0]->[0],
      $start,
      $end,
      $exons[0]->[6],
      $exons[0]->[8],
      $exons[0]->[8],
    );
    my $start_codon = [];
    my $stop_codon = [];
    foreach my $exon(@exons)
    {
      if($exon->[2] eq "Einit")
      {
        if($exon->[6] eq "+")
        {
          $start_codon = [$exon->[3], $exon->[3] + 2];
        }
        else
        {
          $start_codon = [$exon->[4] - 2, $exon->[4]];
        }
        printf
        (
          "%s\tSNAP\tstart_codon\t%lu\t%lu\t.\t%s\t.\tParent=%s.mrna\n",
          $exon->[0],
          $start_codon->[0],
          $start_codon->[1],
          $exon->[6],
          $exon->[8],
        );
      }
      elsif($exon->[2] eq "Eterm")
      {
        if($exon->[6] eq "+")
        {
          $stop_codon = [$exon->[4] - 2, $exon->[4]];
        }
        else
        {
          $stop_codon = [$exon->[3], $exon->[3] + 2];
        }
        printf
        (
          "%s\tSNAP\tstop_codon\t%lu\t%lu\t.\t%s\t.\tParent=%s.mrna\n",
          $exon->[0],
          $stop_codon->[0],
          $stop_codon->[1],
          $exon->[6],
          $exon->[8],
        );
      }
      elsif($exon->[2] eq "Esngl")
      {
        if($exon->[6] eq "+")
        {
          $start_codon = [$exon->[3], $exon->[3] + 2];
          $stop_codon = [$exon->[4] - 2, $exon->[4]];
        }
        else
        {
          $start_codon = [$exon->[4] - 2, $exon->[4]];
          $stop_codon = [$exon->[3], $exon->[3] + 2];
        }
        printf
        (
          "%s\tSNAP\tstart_codon\t%lu\t%lu\t.\t%s\t.\tParent=%s.mrna\n",
          $exon->[0],
          $start_codon->[0],
          $start_codon->[1],
          $exon->[6],
          $exon->[8],
        );
        printf
        (
          "%s\tSNAP\tstop_codon\t%lu\t%lu\t.\t%s\t.\tParent=%s.mrna\n",
          $exon->[0],
          $stop_codon->[0],
          $stop_codon->[1],
          $exon->[6],
          $exon->[8],
        );
      }
      $exon->[2] = "exon";
      $exon->[8] = "Parent=". $exon->[8] .".mrna";
      printf("%s\n", join("\t", @$exon));
    }
    @exons = ();
  }
}