#!/usr/bin/perl
use strict;
use warnings;
use feature qw/ say /;

my %hash;
$hash{'rna1'}{'dna1'} = '1111';
$hash{'rna1'}{'dna2'} = '1111';
$hash{'rna2'}{'dna1'} = '2222';
$hash{'rna3'}{'dna1'} = '2222';
$hash{'rna3'}{'dna2'} = '4444';
$hash{'rna2'}{'dna3'} = '3333';

say 'Report by RNA:';
foreach my $rna ( sort keys %hash ) { 
  say "  $rna has:";
  foreach my $dna ( sort keys %{$hash{$rna}} ) { 
    say "    $dna = $hash{$rna}{$dna}";
  }
}
say ''; 

# reverse the hash
my %hash2 = %hash;
foreach my $key ( keys %hash2 ) { 
  while ( my ( $subkey, $value ) = each %{ $hash2{$key} } ) { 
    $hash2{ $subkey }{ $key } = $value;
  }
  delete $hash2{ $key };
}

say 'Report by DNA:';
foreach my $dna ( sort keys %hash2 ) { 
  say "  $dna is in:";
  foreach my $rna ( sort keys %{$hash2{$dna}} ) { 
    say "    $rna with $hash2{$dna}{$rna}";
  }
}
say ''; 

__END__