[Bioperl-l] .qual are like fasta files

[Hilmar Lapp]

Ewan Birney wrote:
> 
> Chad -
> 
> All this sounds great! Good stuff!
> 
> i think the deliberate copying of PrimarySeq to PrimaryQual is fine. I
> would put it in
> 
> Bio::Seq::PrimaryQual
> 

I agree.

> I suspect inherieting from Bio::PrimarySeqI is probably a bad idea. open
> quesiton what one does with trunc. translate is not possible ;)
> 
> We really need a Bio::IdentifiableI interface that it could inheriet for
> the identifier set.
> 
> After than I would make a
> 
> Bio::Seq::SeqWithQuality
> 
> which would inheriet from Bio::Seq (hence have a Bio::PrimarySeq and
> all the other goodies) but have in addition a Bio::Seq::PrimaryQual, and
> give access to the quality values in many places.

That's actually a good idea. I had this mingled into one module,
but separating and then merging by inheritance is better I agree.
Still, you need to overwrite trunc() and revcom() then for
consistency (truncate etc seq /and/ qualvals).

	-hilmar
-- 
-----------------------------------------------------------------
Hilmar Lapp                              email: hilmarl@yahoo.com
A-1120 Vienna
-----------------------------------------------------------------