use Bio::SearchIO.
my $fh;
open($fh, "fasta34 query.pep db |");
my $in = Bio::SearchIO->new(-format => 'fasta', -fh => $fh);
while( my $r = $in->next_result ) {
 while( my $hit = $r->next_hit ) {
   while( my $hsp = $hit->next_hsp ) {
   }
 }
}