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my $seqio = Bio::SeqIO->new(-format => $seqformat, -file =>$filename);
while( my $seq = $seqio->next_seq ) {
...
       " desc is ", $seq->description(), "\n";
 print "sequence is ", $seq->seq(), "\n";
}

my $fh = Bio::SeqIO->newFh(-format =>$seqformat, -file =>$filename);
while(<$fh>) {
 my $seq = $_;
 # do as before
}

my $fh;
open($fh, "cat seqfile |") ||die $!;
...
 #and so forth....
}