[Bioperl-l] Question on seqfeature mapping

Lajus Florian flajus at labri.fr
Wed Feb 8 04:52:04 EST 2012


Never mind. It works much better if write: 
"Bio::Annotation::SimpleValue<=>Bio::SeqFeatureI instead.

The problem is if we also want to find by primary_tag:
my $query = Bio::DB::Query::BioQuery->new(
-datacollections => ["Bio::Annotation::SimpleValue<=>Bio::SeqFeatureI qv"],
-where => ["Bio::Annotation::SimpleValue::tagname = \'$tag\'","qv.value 
= \'$value\'","Bio::SeqFeatureI.primary_tag = ".$term_primary_key]);

The slot type_term_id is not mapped to column for table seqfeature

Le 08/02/2012 09:02, Lajus Florian a écrit :
> 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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