# pseudocode

my %report;

foreach my $line( $fh_one ){
 if... matching..
   extract the part interesting

   $report{  $interesting_part  }[0] = 1;  # first file populates the element 0


foreach my $line( $fh_two ){
 if... matching..
   extract the part interesting

   $report{  $interesting_part  }[1] = 1;  # first file populates the element 1 

   
# result like

%report = (

    interesting1 = [ undef, 1 ], # is present only in the second file
    interesting2 = [ 1, undef ], # is present only in the first file
    interesting3 = [ 1, 1 ],     # is present in both files
);