Hi, With a limited information given i have put together a script. Maybe you can use it to improve yours.

use strict;
use warnings;


open( my $fh, '<', "input.txt" ) or die "Cannot open input file: $!";
chomp ( my @input_data = <$fh> );
close($fh);

open( my $frh, '<', "reference.txt" ) or die "Cannot open reference fi
+le: $!";
chomp ( my @ref_data = <$frh> );
close ($frh);

my @output = map {
    my $value = $_;
    grep { $value eq $_ } @ref_data;
} @input_data;

open ( my $wh, '>', "output.txt" ) or die ( "Cannot open the output fi
+le. $!");

print {$wh} $_ for @output;
close($wh);
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