[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?

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?

: Hilmar Lapp -:- Durham, NC -:- hlapp at drycafe dot net :

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