my %tags;
while(<$input_file_descriptor>){
  # do stuff to skip headers and blank lines
  chomp;
  my( $tag, $freq ) = split /\s+/;
  $tags{$tag} = $freq;
}

for my $tag (sort { $tags{$b} <=> $tags{$a} } keys %tags ){
  my $freq = $tags{$tag}; # to clarify things below
  my $unique_string = make_unique_string($tag, $freq);
  print ">$unique_string\t$tag\t$freq\n";
}