[BioSQL-l] FW: SeqWithQuality and biosql

[Marc Logghe]

Apologies for cross posting, I had picked the wrong mail adress :-(

-----Original Message-----
From: Marc Logghe 
Sent: Monday, July 04, 2005 11:43 AM
To: bioperl-l at portal.open-bio.org
Subject: SeqWithQuality and biosql

Hi all,
I am currently exploring the possibility to store a
Bio::Seq::SeqWithQuality object in biosql.
Has anyone ever tried this ?
One possibility would be to
1) split up the Bio::Seq::SeqWithQuality object into a plain
Bio::Seq::RichSeq and a Bio::Seq::PrimaryQual
2) store them separately in biosql; different namespaces
3) link them with a relation term.
4) make a custom adaptor to fetch the persistent objects from biosql and
reconstruct the Bio::Seq::SeqWithQuality

Does that make sense ? Any other suggestions/possibilities ?
As a test I tried to load a Bio::Seq::PrimaryQual in biosql using the
load_seqdatabase.pl but it fails because Bio::Seq::PrimaryQual does not
have a namespace method.
I hope I'm wrong but I have the impression there is a long way to go ;-)

Marc