Hmmm. That looks like homework. You really should state that going in but you deserve kudos for giving it a shot before asking. Given that this is homework, though, I'm only going to give you hints.

First, you should always:

use strict;
use warnings;
use diagnostics;
[download]

Next, you probably want to use the 3-argument version of open:

open(INFO, "<", "$infile") or die ("could not open file to append".$!)
+;
open(FILEA, "<", "outputfromvariantparser1.txt") or die ("could not op
+en file to write output");
open(FILEB,">>", output.txt") or die ("could not open file to write ou
+tput");
[download]

You should probably lookup 'open' -- I see a problem with more than one of your files. (hint: one of the translations I did, above, does what your original code did but clearly doesn't do what you intend).

I don't think you want to nest your loops.

You'll need to figure out how to cycle through 'raw_data'

Edit: I made one hint a little clearer.