[Bioperl-l] Problems after changing display_id of a sequence in SimpleAlign

[Jason Stajich]

It has to do with the way the names are kept to handle the idea that  
there can be multiple sequences with same id (the ID is stored as ID/ 
START-END). So changing the ID means it cannot be found without  
updating the hash with the names.

Currently it is generally easier to remove the sequence and re-add it.  
We can add a rename function I suppose -- there should be a way to do  
it via the $aln object but I don't think that API is currently written.

$aln->remove_seq($seq);
$seq->display_id("1");
$aln->add_seq($seq);


On Mar 20, 2009, at 2:09 PM, albezg wrote:

> Hi all,
> I'm trying to change FASTA header(display_id) for a sequence in an
> alignment(SimpleAlign).
>
> There are no issues when I print it, however when I use AlignIO to  
> write
> the alignment to a FASTA file, it does not work. Is this behavior  
> intended?
>
> Demo code: http://github.com/jhannah/sandbox/tree/master/Bio_AlignIO_bug
>
> The error:
> ------------- EXCEPTION -------------
> MSG: No sequence with name [1/1-11]
> STACK Bio::SimpleAlign::displayname
> /scratch/BioSoftware/bioperl-live/Bio/SimpleAlign.pm:2659
> STACK Bio::AlignIO::fasta::write_aln
> /scratch/BioSoftware/bioperl-live/Bio/AlignIO/fasta.pm:200
> STACK toplevel ./demo.pl:14
> -------------------------------------
>
> Alexandr
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Jason Stajich
jason at bioperl.org