A perl script which finds strings of file1(fromFile) against file2(toFile).

findStr.pl

use strict;
use warnings;
use Getopt::Long;

my $notExist = 0;
my $fromFile;
my $toFile;

GetOptions(
  'notExist'   => \$notExist,
  'fromFile=s' => \$fromFile,
  'toFile=s'   => \$toFile,
) or die 'Usage: findStr.pl {-f|fromFile} <Keyword file> {-t|toFile} <target file> [-n|notExist]';

open(my $fromFh, "< $fromFile") or die "Can't open $fromFile: $!";
open(my $toFh, "< $toFile")     or die "Can't open $toFile: $!";

while (my $checkLine = <$fromFh>) {
    next if ($checkLine =~/^#/);
    chomp($checkLine);
    
    my $found = 0;
    while (my $tgtLine = <$toFh>) {
        next if ($tgtLine =~/^#/);
        
        # I should't use regular expressions here.
        my $checkLineQuoted = quotemeta($checkLine);
        
        # If $tgtLine has a pattern of $checkLineQuoted.
        if ($tgtLine =~/$checkLineQuoted/) {
            $found = 1;
            last;
        }
    }
    # Perl keeps a position of $toFh even if a while loop ends, so it is necessary to seek the position to the begining of the target file.
    seek($toFh, 0, 0);
    
    if ($notExist) { # Not found string.
        if ($found == 0) {
            print "$checkLine\n";
        }
    }
    else { # Found string.
        if ($found != 0) {
            print "$checkLine\n";
        }   
    }
}

close($fromFh);
close($toFh);