[Bioperl-l] Sequence IDs and Comment()s

[Ewan Birney]

On Tue, 23 Oct 2001, Jason Eric Stajich wrote:

[jasons comments about ids are bang on. It is just a large mess, mainly
due to way a whole host of legacy things work. shucks. What can one do?]

> 
> > General observation: When performing Bio::Seq <-> BSML, I end up with
> > a fistful of objects from one implementation that have no clear
> > corollary in the other. In BSML, there are two generic name/value type
> > containers (e.g. <Attribute name="user" content="Bob"> or <Qualifier
> > value-type="gene" value="actin">) - I've used these liberally to store
> > information that otherwise has no clear home. In the reverse
> > direction, I've been mapping orphaned data into Comment()s of the form
> > "name: Bob". However, I fret about the lack of predictability in
> > delimiter choice (": " vs ":" vs "\t" vs "," etc.).
> >
> > So... What would people think of adding a type() (or class(),
> > category(), meta(), etc.) method to Comment to optionally qualify the
> > contents?
> >


This is just waiting for the new annotation framework to kick in - then
you would have a slot of these attributes (cue - interesting discussion
about each IO system being able to figure out what to do with each slot)


> 
> I'm wary of this because it implies we are starting to interpret the data
> rather than just provide a mechanism for storing it and manipulating it,
> how would this work for a GenBank -> Seq -> BSML trip and back?
> 
> 
> 
> > -Charles
> >
> > Jason Eric Stajich wrote:
> >
> > ...snip...
> >
> > > If you wanted these names printed out with the seqio system you should
> > > make sure and set the display id:
> > > $seq->display_id("myaccessionnumber");
> > >
> > > display id should really not have spaces in it since it is the
> > > intended unique id for the sequence in a db.
> >
> > ...snip...
> >
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
> 
> 
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