use Bio::SeqIO

my $in  = Bio::SeqIO->new(-file => "test.fa" , '-format' => 'Fasta');
my $out = Bio::SeqIO->new(-file => ">out.fa" , '-format' => 'Fasta');
 
while ( my $seq = $in->next_seq() ) { 
  $out->write_seq($seq) if($seq->length > 500);
}