[Bioperl-l] Bio::AlignIO ignores questionmarks?
avilella at gmail.com
Fri Apr 14 10:01:01 EDT 2006
It seems like missing_char is more for SimpleAlign than for AlignIO. So
in case of fasta files with '?' chars, they will be ignores in line 113
So you can add '\?' in that line of fasta.pm.
That will parse it correctly, although I am not sure whether fasta
format should or shouldn't allow '?' chars in the file.
On Thu, 2006-04-13 at 20:38 -0400, Kai Müller wrote:
> 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,
> Kai Müller
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
More information about the Bioperl-l