One of reader at Bioinformatics-made-simple.com asked to me to give a Fgenesh Parser which can process the results obtained from FGENESH server, a gene prediction server from Softberry. Although I didn't get success in gene prediction from multiple sequences in a go, but because of their great collection of genome FGENESH is good server for ORF prediction. So here is a FGENESH parser orginally written by Malcolm.Cook 


FGENESH parser.pl

#!/usr/bin/env perl

# PURPOSE: parse fgenesh output into gff
# USAGE: fgenesh fish somefish.dna | fgenesh2gff > somefish.dna.fgenesh.gff

use strict;
use warnings;

use Bio::Tools::Fgenesh;    # to parse output into feature
use Bio::Tools::GFF;

# Remaining options should name files to process, but if none, process
# standard input:

@ARGV = ('-') unless @ARGV; 
my $fgenesh = Bio::Tools::Fgenesh->new(-fh => \*ARGV);
my $featureout = new Bio::Tools::GFF(-gff_version=>2);
my $IDNUM = 0;
while (my $gene = $fgenesh->next_prediction()) {
  my $ID =  $gene->seq_id . "_fgenesh_" . ++ $IDNUM;
  $gene->add_tag_value('ID', $ID);
  foreach ($gene->features) {
    $_->add_tag_value('Parent', $ID);
    $_->seq_id($gene->seq_id);
    $featureout->write_feature($_);
  }
}
$fgenesh->close();    
exit 0;

fgenesh.pl yourinput.txt > yourresult.gff

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