[Bioperl-l] Gbrowse/BioSQL question

[Marc Logghe]

> BTW, this seems to work fine for the namespace ! You can 
> query multiple namespaces for a certain accession by setting 
> biodbname to % in the conf file.
> 
Correction: just found out that you can set it to whatever you want; even leave it out. The namespace seems not to be taken into account at all, all of them are queried.
This is a problem when you have different versions sitting in different namespaces:

MSG: Unique key query in Bio::Das::BioSQL::PartialSeqAdaptor returned 2 rows instead of 1. Query was [version="0",accession_number="ZK822.4"]
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:960
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.6.1/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:856
STACK Bio::Das::BioSQL::PartialSeqAdaptor::find_by_unique_key /usr/lib/perl5/site_perl/5.6.1/Bio/Das/BioSQL/PartialSeqAdaptor.pm:22
STACK Bio::Das::BioSQL::BioDatabaseAdaptor::fetch_Seq_by_accession /usr/lib/perl5/site_perl/5.6.1/Bio/Das/BioSQL/BioDatabaseAdaptor.pm:129
STACK Bio::Das::BioSQL::get_feature_by_name /usr/lib/perl5/site_perl/5.6.1/Bio/Das/BioSQL.pm:201
STACK Bio::Graphics::Browser::_feature_get /usr/lib/perl5/site_perl/5.6.1/i386-linux/Bio/Graphics/Browser.pm:1416
STACK Bio::Graphics::Browser::name2segments /usr/lib/perl5/site_perl/5.6.1/i386-linux/Bio/Graphics/Browser.pm:1341
STACK main::lookup_segments /var/www/cgi-bin/gbrowse:1261
STACK main::get_segments /var/www/cgi-bin/gbrowse:1224
STACK toplevel /var/www/cgi-bin/gbrowse:168