[Bioperl-l] Bio::SeqIO::fasta id printing

[Ewan Birney]

On Thu, 7 Jun 2001, Jason Stajich wrote:

> [ Warning: Boring bioperl sequence objects internals ]
> 
> Bio::SeqIO::fasta prints a sequence using $seq->id() which is mapped to
> display_id in bioperl.  However in ensembl, which uses the PrimarySeqI.pm
> model, they have an id() method which refers to their internal id for the
> sequence object.  I would propose we change Bio::SeqIO::fasta to print
> the id with $seq->display_id() unless there is a fundamental reason for
> using the id() call in fasta.pm.

probably a good idea.

> 
> In looking at these methods I'm also confused why there is implementation
> in PrimarySeqI and PrimarySeq for the id() method since it is just
> aliased to display_id in both modules.  
> 

cruft. But alot of code expects

   $seq->id()

to work (hang over from the 0.4 series etc)

so we need this to happen somewhere, probably in PrimarySeqI...


> References:
>   Bio::SeqIO::fasta.pm v1.23 line:168
>   Bio::PrimarySeqI v1.29 line 629
>   Bio::Seq.pm v1.38 line 480
> 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------