Perhaps. Alternatively, can you share some example data? I've been using the following to check if what I wrote worked:

. ignored
> someidentifier
. ignored
ATATATATGC
. ignored
> someidentifier2
. ignored
GCGCGCGCAT
[download]

This yields:

$ perl 1093455.pl
> someidentifier, 20
> someidentifier2, 80
$
[download]

Which is what I expected.

(Side note -- I don't know anything about bioinformatics, or how FASTA files are usually structured, so this may well be a nonsensical file; I merely inferred what it might look like from the script you posted yourself.)