OK, I can't read your code easily, and I don't really feel like trying. If what you want is "all lines found in file1 which are not in file2" then here you go: 
#!/usr/bin/perl
use strict;

my ($source_filename,$exclusion_filename) = @ARGV;

# read each line of exclusion file and store as a hash-key (for quicke
+r look-up)
open EXCLUSION, "$exclusion_filename" or die "Could not open file of e
+xcluded lines: $!\n";
my %exclude = map { ($_ => 1) } <EXCLUSION>;
close EXCLUSION;

open SOURCE, "$source_filename" or die "Could not open source file: $!
+\n";
while (<SOURCE>) {
    print unless $exclude{$_};
}
close SOURCE;

[download]
Results: 
[me@host scratch]$ cat > a
asdf
asdf
fdsa
asd
ddd
d
[me@host scratch]$ cat > b
ddd
as
[me@host scratch]$ perl tmp.pl a b
asdf
asdf
fdsa
asd
d
[me@host scratch]$

[download]

------------
:Wq
Not an editor command: Wq

In reply to Re: Comparing files by etcshadow
in thread Comparing files 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.