cal free energy

gistfile1.txt

sub add_free_energy{
  my $gb = shift;
  for my $cds ($gb->feature('CDS')){
    my $before = $gb->before_startcodon($cds,4);
    my $after = substr ($gb->get_geneseq($cds), 0 , 30);
    my $freeenergy = `echo "$after" | hybrid-ss-min --stream`;
    chomp $freeenergy;
    $gb->{$cds}->{'free_energy'} = $freeenergy;
  }
  return $gb;
}

#gb = add_free_energy($gb);