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my %file_genes = %$file_gene_ref;
...
...
...
    $intersection{$_} = $hash1{$_} if exists $hash2{$_};
...

    $intersection{$_} = $file_gene_ref->{$m1}{$_}
        if exists $file_gene_ref->{$m2}{$_};

  %hash1 = %{$file_gene_ref->{$m1}};
  %hash2 = %{$file_gene_ref->{$m2}};