[BioSQL-l] How to get a Seq object from Bio::DB::Persistent::Seq

[Daniel Lang]

Thank you both for your extensive and quick answers answers...

Hilmar Lapp wrote:
 >
 > On Jun 2, 2004, at 2:31 AM, Marc Logghe wrote:
 >
 >> Hi Daniel,
 >>
 >>> I want to copy the object into a fresh seq object, to add new data and
 >>> store it afterwarts as a new entry with a different namespace.
 >>
 >>
 >> I don't know what will happen if you change the namespace of the
 >> persistent object and store it. Probably a lot of constraints ;-)
 >> (Not  tested though !)
 >> A route you could follow is to
 >> 1. fetch the plain seq object
 >
 >
 > You don't really need to do this even.
 >
 >> 2. change the namespace and add some features
 >> 3. make it persistent and
 >> 4. store it.
 >>
 >
 > Right, that would be the way.
 >
 >> suppose you have your persistent seq in $pseq;
 >> my $seq = $pseq->obj;
 >> $seq->namespace('my_new_namespace')
 >>
 >
 > Again, no real reason to get the wrapped object unless you explicitly
 > need a non-persistent object.
 >
 > Persistent objects in bioperl-db speak are not tightly coupled to the
 > database; in fact you might say they are uncoupled. What I mean is that
 > you may change any attribute or property of the persistent object
 > without having any effect on what is stored in the database. Only once
 > you ask the object to store itself will it sync the changes to the
 > database.
 >
 > So, you may simply do the following:
 >
 >     while (my $pseq = $query->next_object) {
 >         # e.g. change namespace
 >         $pseq->namespace("my namespace");
 >         # change other things, e.g., tack on another feature
 >         # (which may or may not be a persistent object)
 >         $pseq->add_SeqFeature($myfeature);
 >         # ...
 >         # when done making changes, sync to database
 >         $pseq->store();
 >     }
 >
 > Note that this will update bioentries to change their namespace, not
 > duplicate them in another namespace. If you wanted to duplicate a
 > sequence in another namespace, possibly with some changes on the
 > annotation, replace $pseq->store() with the following:
 >
 >         ...
 >         # trigger insert by making the object forget
 >         # its primary key
 >         $pseq->primary_key(undef);
 >         # we need to duplicate dependent objects
 >         # (children) too, like features
 >         foreach my $pfea ($pseq->get_SeqFeatures) {
 >             $pfea->primary_key(undef)
 >                 if $pfea->isa("Bio::DB::PersistentObjectI");
 >             # features have locations
 >             $pfea->location->primary_key(undef)
 >                 if $pfea->location->isa("Bio::DB::PersistentObjectI");
 >         }
 >         # do the insert
 >         $pseq->create();
 >
 > You will note that this sample code actually does not cover all
 > possible cases; e.g., if there are sub-features, or split locations.
 > But you get the idea. Nevertheless, there is indeed a case for having a
 > convenience method for de-persisting objects to better support those
 > who want to duplicate them.
 >
 >> # do some other stuff
 >>
 >> my $new_pseq = $db->create_persistent($seq);
 >> $new_pseq->create;
 >>
 >
 > Note that this has problems associated as outlined above:
 >
 >     - if you wanted to update the sequence, this would not do that
 >     - you will update the features though so that the original sequence
 > won't have any features anymore (a feature has a foreign key to exactly
 > one bioentry)
 >
 >>>
 >>> Additionally, I'm quite confused by the mapping of bioperl objects to
 >>> biosql tables(e.g. for generating a Bio:Query with datacollections):
 >>> connections like bioenty<->seqI are obvious, but the rest?
 >>> Is there a something like a overview list of the object mapping?
 >>
 >> Have a look at  perldoc -m Bio::DB::BioSQL::BaseDriver, more
 >> precisely  at the %object_entity_map variable.
 >> Examples of queries you might find in
 >> http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-db/t/
 >> query.t?rev=1.9&cvsroot=bioperl&content-type=text/vnd.viewcvs-markup
 >> and also the presentation given at BOSC2003:
 >> http://open-bio.org/bosc2003/slides/Persistent_Bioperl_BOSC03.pdf
 >>
 >
 > Right. Thanks for helping Marc.
 >
 >     -hilmar
 >

-- 

Daniel Lang
University of Freiburg, Plant Biotechnology
Sonnenstr. 5, D-79104 Freiburg
phone: +49 761 203 6988
homepage:  http://www.plant-biotech.net/
e-mail: daniel.lang at biologie.uni-freiburg.de

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