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my %hash;  # somewhere before you start to loop over the data
...
# within the loop over your data
...
  label => $label,
};
$hash{$signature} = $structure;  # save it

for my $signature (keys %hash) {
  my $structure = $hash{$signature};
  printf "%s|%s\n%s\n%s\n",
...
      $structure->{sequence},
      $structure->{label};
}