[BioSQL-l] Help with load_seqdatabase.pl

[Jansen E Lim]

Hello,

I seem to be having trouble using the -lookup option of
load_seqdatabase.pl script.  In particular, I wanted to see what
the option
would
do as documented as follows:
            --lookup
            flag to look-up by unique key first, converting the
insert
            into an update if the object is found

I also tried using --lookup 1 without success.  I have no trouble
using  -noupdate and -remove option with -lookup.

Here's how I invoke the script:  load_seqdatabase.pl  -dbname
refseq -driver Pg -lookup -format genbank dup.dat
Here's the error message I get:

DBD::Pg::st execute failed: ERROR:  Cannot insert a duplicate key
into unique index comment_bioentry_id_key at
/libpath/Bio/DB/BioSQL/BaseDriver.pm line 564, <GEN0> line 116.

-------------------- WARNING ---------------------
MSG: insert in Bio::DB::BioSQL::CommentAdaptor (driver) failed,
values were ("PROVISIONAL REFSEQ: This record
has not yet been subject to final NCBI review. The reference
sequence was derived from J04733.1. ","1") FKs (3)
ERROR:  Cannot insert a duplicate key into unique index
comment_bioentry_id_key
---------------------------------------------------
NOTICE:  current transaction is aborted, queries ignored until
end of transaction block
DBD::Pg::st fetchall_arrayref failed: no statement executing at
/stf/biocgi/limje/Bio/DB/BioSQL/BasePersistenceAdaptor.pm line
801, <GEN0> line 116.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not store NM_012500:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: create: object (Bio::Annotation::Comment) failed to insert
or to be found by unique key
STACK: Error::throw
STACK: Bio::Root::Root::throw
/stf/sys64/perl/newlib/Bio/Root/Root.pm:342
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
/stf/biocgi/limje/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:197
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
/stf/biocgi/limje/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:240
STACK: Bio::DB::Persistent::PersistentObject::store
/stf/biocgi/limje/Bio/DB/Persistent/PersistentObject.pm:266
STACK:
Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
/stf/biocgi/limje/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:220

STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::create
/stf/biocgi/limje/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:205
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
/stf/biocgi/limje/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:240
STACK: Bio::DB::Persistent::PersistentObject::store
/stf/biocgi/limje/Bio/DB/Persistent/PersistentObject.pm:266
STACK: Bio::DB::BioSQL::SeqAdaptor::store_children
/stf/biocgi/limje/Bio/DB/BioSQL/SeqAdaptor.pm:179
STACK: Bio::DB::BioSQL::BasePersistenceAdaptor::store
/stf/biocgi/limje/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:260
STACK: Bio::DB::Persistent::PersistentObject::store
/stf/biocgi/limje/Bio/DB/Persistent/PersistentObject.pm:266
STACK: ../load_seqdatabase.pl:400
-----------------------------------------------------------


STACK: Error::throw
STACK: Bio::Root::Root::throw
/stf/sys64/perl/newlib/Bio/Root/Root.pm:342
STACK: ../load_seqdatabase.pl:409
-----------------------------------------------------------

Thanks for helping out.

-Jansen