You need to specify a 'mode' when you use open. This means that you specify whether you want to read from or write to a particular file (you can do both, but you don't need that for now).

use strict;
use warnings;

my $INPUT;
my $OUTPUT;

open($INPUT, "<", "my_input_file.txt"); #the "<" tells it you want to 
+read from the file
open($OUTPUT, ">" "my_output_file.txt"); #the ">" tells it you want to
+ write to the file.

while(my $line=<$INPUT>){
     #.. do some changes to $line ..
     print $OUTPUT $line #prints $line (after I've done whatever chang
+es) to the file I opened as $OUTPUT
}
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check out here for some more info on filehandles. Also bear in mind that you can either not declare a filehandle, and just use a plain text word, e.g.  open(INPUT,"<","input_file.txt); or you can declare a variable as I did in the example above. IMO it's a better habit to get into to use a variable, as you start to get into trouble when/if you try to pass filehandles around subs (later..!)