[Bioperl-l] SeqWithQuality and biosql

Marc Logghe Marc.Logghe at devgen.com
Mon Jul 4 05:43:08 EDT 2005

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 ;-)


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