[BioSQL-l] Load seqfeature from biosql database with perl

[Michael Cipriano]

Ah, I think I figured it out.

my $seqfeature_id = '401138';
my $adaptor = $seqdb_obj->get_object_adaptor("Bio::SeqFeatureI");

my $query = Bio::DB::Query::BioQuery->new(

-datacollections=>["Bio::SeqFeatureI t1"],
                                        -where => ["t1.Bio::SeqFeatureI
= ?"]);

my $qres = $adaptor->find_by_query($query,      -name=>'FIND FEATURE BY
SEQ',

-values=>[$seqfeature_id]);

while(my $loc = $qres->next_object())
{
        my $obj = $loc;

        print $obj->primary_key() . "\n";
        print 'location:' . $obj->location->to_FTstring() . "\n";
        $obj->add_tag_value("test", "moretest");
        foreach my $tag ($obj->get_all_tags())
        {
                print " Values for tag $tag: ";
                print join(' ',$obj->get_tag_values($tag));
                print "\n";
        }
        print "------------------\n";

}



This seems to work
On Wed, 2006-02-22 at 16:58 -0800, Michael Cipriano wrote:
> Hello BioSQLers,
> 
> I have a simple question (I hope), Can I easily load a seqfeature from a
> biosql database into a perl Bio::SeqFeatureI object?  I have the
> database value for the  seqfeature.seqfeature_id and would like to load
> it using this alone.
> 
> I do not want to have to load the whole bioentry object then search for
> the feature, I just want the feature object since the bioentry is a
> whole genome and loading that will take more time then necessary. 
> 
> I have searched the documentation and have even tried looking through
> the code for the modules, but could not find an easy fast method.
> 
> Please reply directly to me as well as the list as I am not a list
> member.
> 
> Thanks for your help,
> 
> 
> Michael Cipriano
> 
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