That's going to mangle your lines anyway. You could use:

perl -pe'chomp; END { print "\n" }' file
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Update: Forgot about "inside a Perl script". Well, let's avoid launching a new Perl, then.

open(my $fh_in, '<', $qfn_in)
   or die("Can't open \"$qfn_in\": $!\n");

open(my $fh_out, '>', $qfn_out)
   or die("Can't create \"$qfn_out\": $!\n");

while (<$fh_in>) {
   chomp;
   print $fh_out $_;
}

print $fh_out "\n";
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