There are a few shortcuts that could make this smaller, but the code below is one way to comment lines that matched a list of words.

However, you will probably need to dial in the regex to better meet your needs.

#!/usr/bin/perl

use strict;
use warnings;

my @file_a_array;
my $newfile;
my $file_a = <path to word file>;
my $file_b = <path to lines of text>;

open (FILE_A, "$file_a") or die "couldn't open the file!";

while (my $line = <FILE_A>) {
     chomp ($line);
     push (@file_a_array, $line);
}

close (FILE_A);

open (FILE_B, "$file_b") or die "couldn't open the file!";

while (my $line = <FILE_B>) {
     chomp ($line);
     foreach my $word (@file_a_array) {
        if ($line =~ /$word/) {
                $newfile = $newfile . "# ";
        }
     }
     $newfile = $newfile . $line . "\n";
}

close (FILE_B);

open (FILE_B, ">$file_b") or die "couldn't open the file!";
print FILE_B $newfile;
close (FILE_B);

print "end\n";
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Hope this helps!

Jamie