[Bioperl-l] Re: [BioSQL-l] removing features from a sequence

[Amit Indap]

Thanks Hilmar, this snippet worked:

foreach my $pfeat( $dbseq->remove_SeqFeatures() ) {

    $pfeat->remove();

}
$dbseq->store();
$dbseq->commit();

> Second, $dbseq->store() will only store it; i.e., it will update the
> object and either update or insert all attached objects (like features,
> annotations, etc). If you want to delete attached objects then you need
> to do so explicitly by calling $pobj->remove().

Thanks for clarifying this point. I was a bit confused about whether I
needed to call store or remove. But you are right, I need to
explicitly call remove.

On 10/3/05, Hilmar Lapp <hlapp at gnf.org> wrote:
> Yeah I guess this is one of the gotcha's that deserve better
> documentation. The bioperl-db adaptors will not automatically 'sync'
> the database with an object. The reason is that there are too many
> flavors of what you could possibly want as a user, so instead of making
> decisions for you you need to make explicit what you want; however,
> doing so should be reasonably simple.
>
> So here's what's going on and how you can fix it.
>
> First, $dbseq->remove_SeqFeatures() is a Bio::SeqI method present for
> all SeqI objects, not just persistent ones. Except in a few cases where
> lazy loading is already implemented, methods from the native Bioperl
> API are not overridden for persistent objects; i.e., you can manipulate
> your persistent object to your heart's content and nothing will happen
> to the respective row(s) in the database. You need to say
> $dbseq->store() to let your changes take effect. But see below!
>
> Second, $dbseq->store() will only store it; i.e., it will update the
> object and either update or insert all attached objects (like features,
> annotations, etc). If you want to delete attached objects then you need
> to do so explicitly by calling $pobj->remove().
>
> For example, in your case:
>
>         # ... find $dbseq ...
>         # delete all features from the database
>         # Note: I could use $dbseq->get_SeqFeatures() if I
>         # wanted to keep the features on the in-memory object
>         foreach my $pfeat ($dbseq->remove_SeqFeatures()) {
>                 $pfeat->remove();
>         }
>         # now $dbseq and the object in the db don't have features
>
> Same thing for annotation. You can check out some of the sample closure
> implementations for merging objects provided in the scripts/biosql
> directory of bioperl-db, for instance freshen-annot.pl deletes all
> annotation (in the db) from the existing object.
>
> Hth,
>
>         -hilmar
>
> On Oct 3, 2005, at 10:59 AM, Amit Indap wrote:
>
> > Hi,
> >
> > I was trying to remove features for sequences stored in my BioSQL
> > database. Once I run the code snippet below to remove sequence
> > features, I tested to see if the features really had been removed by
> > running a script that reterieves seq features from bioentries.
> > Unfortunately, the features are still there. I'm still learning my
> > around the Bio::DB API
> >
> > Here is my code to attempts to remove sequence features:
> >
> > foreach  (@accs) {
> >
> >     my $acc = $_;
> >     my $adp = $dbadp->get_object_adaptor("Bio::SeqI");
> >
> >     my $seq = Bio::Seq->new(-accession_number => $acc,
> >                           -namespace => $namespace
> >                           );
> >
> >
> >     my $dbseq = $adp->find_by_unique_key($seq);
> >     warn $acc, "  not found in database $namespace" unless  $dbseq;
> >
> >     $dbseq->remove_SeqFeatures(); # remove seqfeatures
> >
> >     $dbseq->commit();
> >     print LOG "removed all seq features for $acc\n";
> > }
> >
> >
> >
> > --
> > Amit Indap
> > http://www.bscb.cornell.edu/Homepages/Amit_Indap/
> >
> > _______________________________________________
> > BioSQL-l mailing list
> > BioSQL-l at open-bio.org
> > http://open-bio.org/mailman/listinfo/biosql-l
> >
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
>


--
Amit Indap
http://www.bscb.cornell.edu/Homepages/Amit_Indap/