[Bioperl-l] SeqWithQuality and biosql

[Heikki Lehvaslaiho]

Marc,

I have not actually talked about this with Chad, but I've had a long time plan 
to refactor Bio::Seq::SeqWithQuality to inherit from Bio::Seq::MetaI. It does 
not at the moment because Chad was there first. Some time later there were 
some other needs to attach meta information to residues and to avoid having 
several implementations in bioperl I wrote Bio::Seq::MetaI and its 
implementation classes.


I do not know if there are any issues why Bio::Seq::SeqWithQuality could not 
be Bio::Seq::MetaI, but it would be good thing to explore that, and implement 
only one very generic way to store residue-based meta values in biosql.

 -Heikki


On Monday 04 July 2005 10:43, Marc Logghe wrote:
> 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
>
>
>
>
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     _/  _/  _/  Heikki Lehvaslaiho    heikki at_ebi _ac _uk
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