[Biopython-dev] sequence class proposal

[Peter]

On May 22, 2008, Blanca Postigo Jose Miguel wrote:
>> If I understood your terminology correctly, "qualities" is a list of
>> scores, one for each letter in the sequence.
> You're right. I'm sorry, I used them a lot and a reserved them a special place
> in the API, my fault, I will remove it, only the sequence should have a
> relevant place in the API, the rest should be stored as features.

I've asked on the BioSQL mailing list about this sort of "per letter"
annotation.  Currently there is no mechanism to store this sort of
thing in the schema.
http://lists.open-bio.org/pipermail/biosql-l/2008-May/001269.html

However, Hilmar did point out some relevant bits of BioPerl to have a look at:

Hilmar Lapp wrote:
> In BioPerl we have Bio::Seq::SeqWithQuality and the more generic
> Bio::Seq::MetaI.

The BioPerl SeqWithQuality sounds like what you were most interested
in  Jose, although the Meta-Interface may be of relevance too.

Peter