[Bioperl-l] BioQuery failure

[Eric Bazin]

Hi,

I discovered bioperl-db few days ago and i'm very enthusiatic using this
tool but i've got a problem using BioQuery. I would be grateful if
anybody can give me an answer about that.

This a piece of my code:

my $db = Bio::DB::BioDB->new(-database => "biosql",
				 -host     => $host,
				 -dbname   => $dbname,
				 -driver   => $driver,
				 -user     => $dbuser,
				 -pass     => $dbpass,
				 -verbose  => 10,
				 );			
my $query = Bio::DB::Query::BioQuery->new(
	-datacollections=>["Bio::SeqI seq",
		"Bio::Annotation::Reference ref",
		"Bio::Annotation::Reference<=>Bio::SeqI"
		],
	-select=>["ref.authors"],
	-where=>["and", "seq.accession_number='AJ311144'",
		seq.display_id='AAG311144'"]
	);

$query->flag("distinct", 1);

my $adaptor = $db->get_object_adaptor("Bio::Annotation::Reference");
my @tab = $adaptor->find_by_query($query);

I receive this error message:

------------- EXCEPTION  -------------
MSG: slot 'accession' not mapped to column for table bioentry
STACK Bio::DB::Query::BioQuery::_map_slot_to_col
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Query/BioQuery.pm:487
STACK Bio::DB::Query::BioQuery::_map_constraint_slots_to_columns
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Query/BioQuery.pm:369
STACK Bio::DB::Query::BioQuery::_map_constraint_slots_to_columns
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Query/BioQuery.pm:356
STACK Bio::DB::Query::BioQuery::translate_query
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/Query/BioQuery.pm:305
STACK Bio::DB::BioSQL::BaseDriver::translate_query
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm:1182
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_query
/usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:1198
STACK (eval) /var/www/cgi-bin/getentry.pl:97
STACK toplevel /var/www/cgi-bin/getentry.pl:67

-- 
Eric Bazin
Laboratoire "Génome Populations Interactions Adaptation"
UM2 - IFREMER - CNRS  UMR 5171
Université de Montpellier 2
C.C. 63,  bâtiment 24 ;34095 Montpellier Cedex 5
Tel:(0)4-67-14-39-13
Tel perso:(0)6-20-91-49-62
Fax:(0)4-67-14-45-54
http://www.univ-montp2.fr/~genetix
Seminaires internes: http://162.38.181.25/seminaire.html