Bio::SeqIO::fasta provides a width
method to specify how written FASTA records should be formatted:
while (my $seq = $seqin->next_seq) {
$seqout->width($seq->length);
$seqout->write_seq($seq);
}
Or of course if your sequences have some maximum size, you can just put a single
$seqout->width(5000);
or so in before the loop.