[Bioperl-l] Re: bioperl-db

[Mike Muratet]

Hilmar

While you're on the subject of load_seqdatabase, I am experiencing a wierd
problem I need some help solving.

I am loading subsets of Genbank into the database I created with the
script create_mysql_db using the script load_seqdatabase.pl all of which I
downloaded from the links at bioperl.org. (Having these records in mysql
saves me a _ton_ of perl writing and thank you to the folks who did the
development.) Sometimes there is overlap in the sets. For example.....

/usr/local/lib/perl5/site_perl/5.8.4/bioperl-db/scripts/biosql/load_seqdatabase.pl --dbname bioseqdb --format GenBank
--namespace clones --lookup --noupdate accessions.gb
Loading accessions.gb ...
 
-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::SeqAdaptor (driver) failed, values were
("BC029727","20987556","BC029727","Mus musculus zeta-chain (TCR)
associated protein kinase, mRNA (cDNA clone MGC:36162 IMAGE:4925739),
complete cds.","1","ROD") FKs (5,10090)
Duplicate entry '20987556' for key 3
---------------------------------------------------
Could not store BC029727:
------------- EXCEPTION  -------------
MSG: create: object (Bio::Seq::RichSeq) failed to insert or to be found by
unique key
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
/usr/local/lib/perl5/site_perl/5.8.4/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:207
STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
/usr/local/lib/perl5/site_perl/5.8.4/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:253
STACK Bio::DB::Persistent::PersistentObject::store
/usr/local/lib/perl5/site_perl/5.8.4/Bio/DB/Persistent/PersistentObject.pm:270
STACK (eval)
/usr/local/lib/perl5/site_perl/5.8.4/bioperl-db/scripts/biosql/load_seqdatabase.pl:517
STACK toplevel
/usr/local/lib/perl5/site_perl/5.8.4/bioperl-db/scripts/biosql/load_seqdatabase.pl:500
 
The offending key is the GI number, which gets stored (apparently) in the 
identifier column of bioentry. I would expect that the namespace would
confer uniqueness. Further, I might expect that an entry under a new
namespace might supercede the previous reference. However, I am baffled by
the exception when I have set --lookup and --noupdate. I have looked at
the code, and I don't see anything simple. Could it be that the lookup
includes the namespace in the key but the store does not? Am I using it
improperly?

Thanks

Mike