It doesn't quite look like your code matches your request; you don't seem to be removing empty lines, but skipping them.

If what you want to do is to ignore blank lines while reading a file, I would do something like this (note that this code is not tested:

open(my $infile, '<', $inputfile) or die "Could not open $inputfile be
+cause $!\n";

while(<$infile>){
   next if /^\s*$/;
   chomp;  # you don't want the newline, do you?
   #processing follows here...
   }
close($infile);
}
[download]

I'm defining "blank line" to be any line comprising only whitespace characters.

Note that tr or y does not handle character classes (to quote: "Note that tr does not do regular expression character classes such as \d or [:lower:]"; see perlop)

(note that most Monks are paid to review people's code; some pleasant words like "please" would be nice when asking for free services).