I'd suggest using already written modules or looking at code from people who have already solved this problem. Bio::SeqIO for one. See the code in the next_seq method. The beauty is if you want to change the file format to genbank you replace 'fasta' with 'genbank'. 
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

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In reply to Re: How to avoid using array in concatenating string of multiple lines by stajich
in thread How to avoid using array in concatenating string of multiple lines OR How To Read FASTA by monkfan

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