[Bioperl-l] Bio::AlignIO ignores questionmarks?
kaimueller at uni-bonn.de
Thu Apr 13 20:38:00 EDT 2006
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();
my $testout = Bio::AlignIO->new(-fh => \*STDOUT , '-format' => 'clustalw');
Can somebody give me a hint here?
thanks and all the best,
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