use Bio::FASTASequence::File;
my $file = '/path/to/seq.fa';

my $obj = Bio::FASTASequence::File->new($file);
my $result_ref = $obj->get_result();
my $counter = 1;

foreach(keys(%{$result_ref})){
  print $counter,": ",$result_ref->{$_}->getSequence(),"\n";
  $counter++;
}
##</code><code>##

>Seq1 (two lines)
AAAAAAAAAAAAA
CCAAAAAAAAAAA
>Seq2 (two lines)
AAAAAAAAAAAAA
AAAAAAAAAAAAA
>Seq3 (one line)
TTTTTTTTTTTTAACTGAAGATTCGC