use strict;
use warnings;
my $fh;
my $myfile = '/path/to/file/a';
unless (open($fh,"<",$myfile)) {
  die "Can't open $myfile: $!\n";
}
my %delete_words = ();
while (<$fh>) {
  chomp;
  $delete_words{$_}++;
}
close($fh);

##</code><code>##

if (exists($delete_words{$_})) {
  # do nothing
}
else {
  # write to file C
}