use Bio::SeqIO;
my $instream = Bio::SeqIO->new( -file    => 'your_in_file',
                                -format  => 'raw' );
my $outstream = Bio::SeqIO->new( -file   => '>>your_out_file',
                                 -format => 'Fasta' )';
while ( my $sequence = $instream->next_seq() ) {
     $outstream->write_seq( $sequence );
}