[Bioperl-l] Question on seqfeature mapping

Lajus Florian flajus at labri.fr
Wed Feb 8 03:02:32 EST 2012


I'm talking about the interface. I'm far from understanding all the way 
the association is done but for a query like this: my $query = 
Bio::DB::Query::BioQuery->new(				-datacollections => 
["Bio::Annotation::SimpleValue=>Bio::SeqFeatureI qv"],
-where => ["qv::value = \'$value\'"]);

according to the sql generator I have this:
SELECT * FROM seqfeature, term qv WHERE seqfeature.term_id = qv.term_id 
AND qv.=>{bioentry_qualifier_value,seqfeature_qualifier_value}.value = 
'Samatha Carter'

Le 08/02/2012 05:37, Hilmar Lapp a écrit :
> 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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