[Bioperl-l] Question on seqfeature mapping

Hilmar Lapp hlapp at drycafe.net
Tue Feb 7 23:37:32 EST 2012


Hi Florian,

Are you asking about the Bio::DB::Query::BioQuery interface, or an object persistence adaptor in Bio/DB/BioSQL? Either way, the code resolves which table to use by the association that needs to be queried. How these map to association tables is in the %association_entity_map mapping. You'll see that there is one for term => seqfeature, which is mapped to seqfeature_qualifier_value, for example. So if the association is between seqfeature and term, the adaptor will then use that table to access the value column.

Does that make sense?

	-hilmar
 
On Feb 7, 2012, at 2:49 PM, florian lajus wrote:

> Hi,
> I have a problem with bio queries: How can I retrieve from datadabse a seqfeature according to its annotation (tagname and value)?
> The problem coming for value as we have "value"          =>  "=>{bioentry_qualifier_value,seqfeature_qualifier_value,location_qualifier_value}.value",
> in the %slot_attribut_map of the base driver.
> Do you know a solution?
> 

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