[BioSQL-l] problem loading swissprot sequences into bioperl-db.

Thu Dec 8 22:42:05 EST 2005

Thanks Hilmar,

 I am pasting the warnings those I got while loading the sequences of swissprot (sprot45 release).

 -------------------- WARNING ---------------------
 MSG: insert in Bio::DB::BioSQL::ReferenceAdaptor (driver) failed, values were ("","","Submitted (AUG-2003) to the EMBL/GenBank/DDBJ databases.","CRC-FC972BB26FD8615A","","") FKs (<NULL>)
 Duplicate entry 'CRC-FC972BB26FD8615A' for key 3
 ---------------------------------------------------
 Could not store P51028:
 ------------- EXCEPTION  -------------
 MSG: create: object (Bio::Annotation::Reference) failed to insert or to be found by unique key
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:208
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
 STACK Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.6/Bio/DB/Persistent/PersistentObject.pm:272
 STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children /usr/lib/perl5/site_perl/5.8.6/Bio/DB/BioSQL/AnnotationCollectionAdaptor.pm:219
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:216
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
 STACK Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.6/Bio/DB/Persistent/PersistentObject.pm:272
 STACK Bio::DB::BioSQL::SeqAdaptor::store_children /usr/lib/perl5/site_perl/5.8.6/Bio/DB/BioSQL/SeqAdaptor.pm:226
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create /usr/lib/perl5/site_perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:216
 STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store /usr/lib/perl5/site_perl/5.8.6/Bio/DB/BioSQL/BasePersistenceAdaptor.pm:254
 STACK Bio::DB::Persistent::PersistentObject::store /usr/lib/perl5/site_perl/5.8.6/Bio/DB/Persistent/PersistentObject.pm:272
 STACK (eval) /home/soumya/packages/bioperl/cvs_bioperl-db/bioperl/bioperl-db/scripts/biosql/load_seqdatabase.pl:619
 STACK toplevel /home/soumya/packages/bioperl/cvs_bioperl-db/bioperl/bioperl-db/scripts/biosql/load_seqdatabase.pl:602

 --------------------------------------

  at /home/soumya/packages/bioperl/cvs_bioperl-db/bioperl/bioperl-db/scripts/biosql/load_seqdatabase.pl line 632

 Regards,
 Soumyadeep

Hilmar Lapp <hlapp at gnf.org> wrote: Great that it works. If you think the duplicate key warning indicate a 
problem (does a message follow stating that a sequence couldn't be 
loaded?) then you will need to paste them here ...

 -hilmar

On Dec 7, 2005, at 5:06 AM, Soumyadeep nandi wrote:

> Thanks Hilmar,
>
>  Its working fine though I am getting some duplicate key warnings. 
> This warning was not found with sprot42.dat release of swissprot.
>
>  With regards,
>  Soumyadeep
>
> Hilmar Lapp  wrote:
>> old version of Biosql. Instead, download bioperl-db from CVS (main
>> trunk, latest revision).
>>
>>  -hilmar
>>
>> On Dec 5, 2005, at 1:38 AM, Soumyadeep nandi wrote:
>>
>> > Hi Everybody,
>> >
>> > I have been trying to load one of the release of swissprot
>> > ("sprot42"). But while running the script "load_seqdatabase.pl" as
>> > (perl scripts/load_seqdatabase.pl -host localhost -format swiss
>> > swissprot_bioperl /var/database/swissprot/sprot42.dat) where '
>> > swissprot_bioperl' i o! ur local database). I am ending up with some
>> > warning messages as below:
>> >
>> > -------------------- WARNING ---------------------
>> > MSG: moltype: pre v1.0 method. Calling alphabet() instead...
>> > ---------------------------------------------------
>> >
>> > -------------------- WARNING ---------------------
>> > MSG: moltype: pre v1.0 method. Calling alphabet() instead...
>> > ---------------------------------------------------
>> > each_Comment (old style Annotation) on new style
>> > Annotation::Collection
>> > STACK Bio::Annotation::Collection::each_Comment
>> > /usr/lib/perl5/site_perl/5.8.6/Bio/Annotation/Collection.pm:612
>> > STACK Bio::DB::SQL::SeqAdaptor::store
>> > /usr/lib/perl5/site_perl/5.8.6/Bio/DB/SQL/SeqAdaptor.pm:470
>> > STACK toplevel scripts/load_seqdatabase.pl:78
>> > each_Reference (old style Annotation) on new style
>> > Annotation::Collection
>> > STACK Bio::Annotation::Collection::each_Reference
>> > /usr/lib/perl5/site_perl/5.8.6/Bio/Annotation/Collection.pm:570
>> > STACK Bio::DB::SQL::SeqAdaptor::store
>> > /usr/lib/perl5/site_perl/5.8.6/Bio/DB/SQL/SeqAdaptor.pm:477
>> > STACK toplevel scripts/load_seqdatabase.pl:78
>> > each_DBLink (old style Annotation) on new style
>> > Annotation::Collection - use get_Annotations('dblink')
>> > STACK Bio::Annotation::Collection::each_DBLink
>> > /usr/lib/perl5/site_perl/5.8.6/Bio/Annotation/Collection.pm:655
>> > STACK Bio::DB::SQL::SeqAdaptor::store
>> > /usr/lib/perl5/site_perl/5.8.6/Bio/DB/SQL/SeqAdaptor.pm:496
>> > STACK toplevel scripts/load_seqdatabase.pl:78
>> >
>> > -------------------- WARNING ---------------------
>> > MSG: moltype: pre v1.0 method. Calling alphabet() instead...
>> > ---------------------------------------------------
>> >
>> > -------------------- WARNING ---------------------
>> > MSG: moltype: pre v1.0 method. Calling alphabet() instead...
>> > ---------------------------------------------------
>> >
>> > -------------------- EXCEPTION --------------------
>> > MSG: Not a simple location nor a split. Yikes
>> > STACK Bio::DB::SQL::SeqLocationAdaptor::store
>> > /usr/lib/perl5/site_perl/5.8.6/Bio/DB/SQL/SeqLocationAdaptor.pm:169
>> > STACK Bio::DB::SQL::SeqFeatureAdaptor::store
>> > /usr/lib/perl5/site_perl/5.8.6/Bio/DB/SQL/SeqFeatureAdaptor.pm:177
>> > STACK Bio::DB::SQL::SeqAdaptor::store
>> > /usr/lib/perl5/site_perl/5.8.6/Bio/DB/SQL/SeqAdaptor.pm:464
>> > STACK toplevel scripts/load_seqdatabase.pl:78
>> > -------------------------------------------
>> > [soumya at soumyadeep bioperl-db-0.1]$
>> >
>> > Moreover it seems only 119 records are being updated into the
>> > database.
>> >
>> > I am using bioperl-1.4 and bioperl-db-0.1. The sql i am using is
>> > sql/basicseqdb-mysql.sql fr! om bioperl-db-0.1.
>> >
>> >
>> > Any suggestion would be highly appreciated.
>> >
>> > Regards,
>> > Soumyadeep
>> >
>> >
>> >
>> >
>> > ---------------------------------
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>> >
>> -- 
>> -------------------------------------------------------------
>> Hilmar Lapp email: lapp at gnf.org
>> GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
>> -------------------------------------------------------------
>>
>>
>
> Yahoo! Personals
>  Let fate take it's course directly to your email.
>  See who's waiting for you Yahoo! Personals
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------

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