First off, you might want to use @ARGV == 2 and @ARGV == 3 instead of that nasty $#ARGV business. It's "cleaner" and it is easier to understand in my opinion.

Anyway, the problem is that you're not removing the elements from @ARGV, and so the while loop is trying to read them as files.

if (@ARGV == 2) { 
  $result = ">" . pop(@ARGV);  # removes element from @ARGV
  # ...
}

elsif (@ARGV == 3) {
  $result = ">" . pop(@ARGV);
  $name = pop(@ARGV);
  # ...
}
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Jeff[japhy]Pinyan: Perl, regex, and perl hacker, who'd like a (from-home) job
s++=END;++y(;-P)}y js++=;shajsj<++y(p-q)}?print:??;