In addition to davorg's advice above you should also always use both strict and warnings, as they can help you identify many common problems.

If you are searching for the words from file A in file B then you will need a different regex. The code you provided is using the entire file A as the regex.

Here's an example that uses one pattern file, one input file, one output file: 

use strict;
use warnings;

if (@ARGV != 3) {
    print "Usage: $0 <pattern file> <input file> <output file>\n";
    exit;
}

my ($pattern_filename, $source_filename, $dest_filename) = @ARGV;

open my $pattern_fh, '<', $pattern_filename or die "Failed to open $pa
+ttern_filename: $!";
my @tokens = ();
while (my $line = <$pattern_fh>) {
    push @tokens, split /\s/, $line;
}
# Create a pattern with alternation of tokens, wrapped in a non-captur
+ing group,
# and a requires word break before and after the word to prevent match
+ing pieces
# of other words 
my $pattern = '\b(?:' . join('|', @tokens) . ')\b';
print "Search pattern: $pattern\n";

open my $infile, "<",  $source_filename or die "Failed to open $source
+_filename: $!"; 
open my $outfile,">>", $dest_filename   or die "Failed to open $dest_f
+ilename: $!"; 

while(my $line = <$infile>) { 
    if ($line !~/$pattern/) { 
        print "adding: $line"; 
        print $outfile $line; 
    } 
} 
close($infile); 
close($outfile);

[download]

In reply to Re: Search and delete lines based on string matching by imp
in thread Search and delete lines based on string matching by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.