[Bioperl-l] Bio::AlignIO ignores questionmarks?
Albert Vilella
avilella at gmail.com
Fri Apr 14 14:01:01 UTC 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
of Bio::AlignIO::fasta.pm.
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.
Anyone?
Cheers,
Albert.
On Thu, 2006-04-13 at 20:38 -0400, Kai Müller wrote:
> 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
>
>
>
>
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