use Bio::SeqIO;
my $in = Bio::SeqIO->new(-format => 'fasta', -fh => \*DATA);
my $i =1;
while( my $s = $in->next_seq  ) {
 print $i++, " : ", $seq->seq(), "\n";
}
__DATA__
> Seq 1 (two lines)
AAAAAAAAAAAAA
CCAAAAAAAAAAA
> Seq 2 (two lines)
AAAAAAAAAAAAA
AAAAAAAAAAAAA
> Seq 3 (one line)
TTTTTTTTTTTTAACTGAAGATTCGC