You can also use Bio::FASTASequence::File:
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++;
}

[download]


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

[download]

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

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