[Bioperl-l] SeqIO fails on masked sequences

[Marc Logghe]

Hi, 
> my $seq_in  = Bio::SeqIO->new(-format=>$format, -file => $infile);
> my $seq_out = Bio::SeqIO->new(-format=>$format, -file => ">$outfile");
> while (my $seq = $seq_in->next_seq()) {

Guess you can do it by setting the alphabet explicitely:
$seq_in->alphabet('dna'); # or 'rna' or 'protein'

You probably also can pass it directly with the constructor, but did not find that immediately.
Indirectly, you can do it also by setting the alphabet for the factory object and passing the factory object with the Bio::SeqIO constructor.

HTH,
Marc