[Bioperl-l] Bio::AlignIO ignores questionmarks?

[Kai Müller]

hi,

I'm very new to BioPerl and have a maybe silly question.
when using Bio::AlignIO to load a set of sequences, the questionmarks are 
simply lost (they refer to missing characters as opposed to gap characters 
[-] or ambiguity [N]). I thought that 'missing_char()' might help, but it 
didn't (I probably used it the wrong way).

when $filename contains sequences with ????, the following snippet would 
produce an alignment with ???? lost and downstream nucleotide just shifted 
and the resulting length differnces filled by '---' @ 3' end:


my $aln_in = Bio::AlignIO->new(-file => "$filename", '-format' => 'fasta');
	my $aln = $aln_in->next_aln();
	$aln->gap_char('-');
	$aln->missing_char('?');
	
	my $testout = Bio::AlignIO->new(-fh => \*STDOUT , '-format' => 'clustalw');
	$testout->write_aln($aln);



Can somebody give me a hint here?

thanks and all the best,

Kai Müller