Code:
open(IN,$annotationfile) or die "Can't open $annotationfile\n";
while(<IN>){
    chomp;
    @data = split(/\t/,$_);
    $Column1 = @data[0];
    $Column2 = @data[1];
    $Column3 = @data[2];
    $Column4 = @data[3];
    $Column5 = @data[4];
    $Column6 = @data[5];
    $Column7 = @data[6];
    $Column8 = @data[7];
    $Column9 = @data[8];
    $Column10 = @data[9];
    $Column11 = @data[10];
print "$Column1\t$Column2....\t$Column11\n";

foreach $_ (1..$#data){
$GOHash{"$Symbols"}{"$GO_Names"} = "$IDs";
foreach $Symbols (@data) {
foreach my $name (sort {$a <=> $b} (keys %GOHash) ) {
    foreach my $annotation (keys %{ $GOHash{$name} }) {
    print "$name, $annotation: $GOHash{$name}{$annotation}\n";
close(IN);
}
}
}
}
}