Text 1:

Entry 1
1 N
2 D
EOE

##</code><code>##

Text 2:

Entry 3
6 N
7 
EOE
Entry 5
4 D
9 D
EOE

##</code><code>##

use strict;
use warnings;
my (@data1,@data2);
my (@array,@array2);

open my $fh, '<', 'Text1' or die "Could not open file to read:$!";
while (<$fh>) {
        if (/^\Entry (\w+)/../\EOE/){
		push @array, $_;
		if (/^(\Entry)/){	
        	push @data1 ,$1;
                	}
	}
}

open $fh, '<', 'Text2' or die "Could not open file to read:$!";
while (<$fh>) {

	if (/^\Entry (\w+)/../\EOE/){
		push @array2, $_;
	       	if (/^(\Entry)/){
		push @data2 , $1;
   		 		}
	}
}
print @array2;
my $size = @data1 < @data2 ? @data1 : @data2; 
my $result= @data1 < @data2 ? "File 1 has missing data" : "File 2 has missing data";
my $ori = @data1 == @data2 ? 1:0;
my $i;
for( $i = 0; $i < $size; $i++){
       if ($data1[$i] ne $data2[$i]){
        printf "%s is mismatch with %s\n",$data1[$i],$data2[$i];
       }
       else {
       &compare();
}
}
print "$result\n" if (!$ori);