[Bioperl-l] Re: [BioSQL-l] (no subject)

[Hilmar Lapp]

On 11/6/03 1:26 AM, "matthieu CONTE" <m_conte at hotmail.com> wrote:

> Hello,
> 
> We just transfered  Arabidospsis Thaliania’s EMBL sequences via SwissProt in
> BioSQL format.
> We are able to take out sequences and annotations (using a
> Bio::DB::PersitenceAdaptorI and the “find_by_unique_key” method) from a
> BioentryID.
> But from an entry, we are unable to take out the access number Pfam, Prosite
> and others... from  the crossreferences table (BioentryDbxref).
> 
> Could you please tell us wich adaptor can we use and how to do it ?
> 
> In short, how can we use the Bio ::DB:: ...adaptor to access to all the
> tables in a BioSQLformat?!!
> 

Generally speaking, you use adaptors to pull objects out or get objects into
the database, the idea being you don¹t have to care a lot about which tables
are involved.

Since you don't exactly explain what you're trying to do, there's multiple
answers and I'll give you three, hoping to hit a match with at least one.

A) If all you know is the database and accession of the dbxref, you can pull
it out by a unique key query:

    $dbxref = Bio::Annotation::DBLink->new(-dbname => 'Genbank',
                                           -primary_id => 'BC6256426');
    $adp = $db->get_persistence_adaptor($dbxref);
    $found = $adp->find_by_unique_key($dbxref);

B) If you want to pull out all dbxrefs of a sequence entry, and you have the
seq object in hand, all annotation will have been loaded. Hence,

    $seq = < ... e.g., find by unique key ...>
    @dblinks = $seq->annotation->get_Annotations('dblink');

Will do the job.

C) Same as B) but you don't have the seq object and you don't want it
either.

    $query = Bio::DB::Query::BioQuery->new(
               -datacollections => ["Bio::SeqI s",
                                    "Bio::Annotation::DBLink dbx",
                                    "Bio::SeqI<=>Bio::Annotation::DBLink"],
               -where => ["s.accession_number = 'BC236452'"]);
    $adp = $db->get_persistence_adaptor("Bio::Annotation::DBLink");
    $result = $adp->find_by_query($query);
    while(my $dbx = $result->next_object()) {
        # do something with $dbx
    }

I may have forgotten a parameter or so, especially for C), check out the
documentation in Bio::DB::PersistenceAdaptorI (and possibly also
Bio::DB::BioSQL::BasePersistenceAdaptor, the base class for all
implementors).

Hth,

    -hilmar

> Many thanks in advance,
> 
> M
> 
> 
> 
> 
> Matthieu CONTE
> 23 route d'EUS
> 66500 CATLLAR
> Tel
> 0468962854
> m_conte at hotmail.com
> 
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-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------