[Biopython-dev] about the SeqRecord and SeqFeature classes

[Jose Blanca]

Hi:

> > To do that in a proper way I would like to use property, that's why I was
> > asking for the possibility of transforming SeqRecord and Seq in new style
> > classes.
>
> Oh I see - then you could put the length check in the property set method?

That's exactly right.

> Would you like to file an enhancement bug for transforming SeqRecord
> and Seq into new style classes, and prepare a patch (for this only)?
> If this doesn't cause any problems with the unit tests then I don't
> foresee any problems getting that change made.
I will, although first I have to look how to do it. I think that I have to 
take a look at your developer docs.

> Style is often debatable.  Sequence is quite long, and seq is fairly
> clear.  Qual on the other hand could be short for qualifier (a term
> used in feature annotation).
I see, you've got a point there.

> I haven't had to deal with 454 or solexa sequence data yet (but I am
> hoping to in the next six months).
I'm exactly working on that right now.

> Given there are lots of possible 
> implementation/object structure ideas, I think it might be premature
> to pick one for Biopython right now.  Would you be happy with the
> SeqRecord __getitem__ method (Bug 2507) and creating the subclassed
> SeqRecord with quality in your own code?  If you find that works well
> in real usage, it would be encouraging for us to use it Biopython.
That's a great way to do it.

> Or 
> have you already been using something like this for serious data
> analysis?
Not yet.

Best regards,

-- 
Jose M. Blanca Postigo
Instituto Universitario de Conservacion y
Mejora de la Agrodiversidad Valenciana (COMAV)
Universidad Politecnica de Valencia (UPV)
Edificio CPI (Ciudad Politecnica de la Innovacion), 8E
46022 Valencia (SPAIN)
Tlf.:+34-96-3877000 (ext 88473)