[BioSQL-l] Problems with load_seqdatabase and genbank files

[albert vilella]

Ok,

I had downloaded the latest version of biosql-schema and bioperl-db with
cvs but I must had done something wrong because I didn't have the latest
version.

I downloaded and installed the tar.gz files linked from the viewcvs of
the project and there was no problem them.

Now I can populate the biosql database with genbank files.

I still have the same problem with swissprot files:

For example, if I try to enter a file with the first 3 entries of
sprot41.dat,

$ ./load_seqdatabase.pl /data/database/minisprot41.dat -format swiss

------------- EXCEPTION  -------------
MSG: swissprot stream with no ID. Not swissprot in my book
STACK Bio::SeqIO::swiss::next_seq
/usr/lib/perl5/site_perl/5.8.0/Bio/SeqIO/swiss.pm:179
STACK toplevel ./load_seqdatabase.pl:396
                                                                                                                            
--------------------------------------

This happens with the lattest version of bioperl-live, bioperldb and
biosql-shema.

Thanks for you help,

Albert

On Tue, 2003-06-10 at 20:30, Hilmar Lapp wrote:
> > -----Original Message-----
> > From: albert vilella [mailto:vilella at bio.ub.es] 
> > Sent: Tuesday, June 10, 2003 10:03 AM
> > To: biosql-l at open-bio.org
> > Subject: [BioSQL-l] Problems with load_seqdatabase and genbank files
> > 
> > 
> > Hello everybody,
> > 
> > I am trying to populate a database(biosql) with a little 
> > GenBank sequence file using load_seqdatabase.pl (redhat linux).
> > 
> > I seems to be parsing the file correctly, but when it starts 
> > to store the entries, it fails with the following error:
> > 
> > Loading /data/database/10014.gbk ...
> > DBD::mysql::st execute failed: Table 'biosql.term' doesn't 
> 
> If you did instantiate the latest version of biosql then this message
> should not occur. It is a clear indication that you are trying to run
> off of an old schema version. If you type the following in the mysql
> shell, what do you see?
> 
> 	mysql> show tables like 'term%'; # should show 5 tables
> 	mysql> describe term;            # should show the table's
> columns
> 	mysql> describe ontology_term;   # should raise an error
> 
> It also seems you did not configure MySQL to enable the InnoDB table
> handler. Check the INSTALL document for how to do this. If you issue in
> mysql
> 
> 	mysql> show variables like 'have_innodb';
> 
> You should get 1 row and 'YES' in the right column if you have
> successfully enabled InnoDB.
> 
> 	-hilmar
> 
> > exist at 
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAdaptor.pm
> > line 903, <GEN0> line 599.
> > DBD::mysql::db rollback failed: Warning:  Some 
> > non-transactional changed tables couldn't be rolled back at 
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BaseDriver.pm 
> > line 1649, <GEN0> line 599. Could not store NC_001321:
> > ------------- EXCEPTION  -------------
> > MSG: error while executing statement in
> > Bio::DB::BioSQL::SimpleValueAdaptor::find_by_unique_key: 
> > Table 'biosql.term' doesn't exist STACK 
> > Bio::DB::BioSQL::BasePersistenceAdaptor::_find_by_unique_key
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> > aptor.pm:909
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::find_by_unique_key
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> > aptor.pm:820
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> > aptor.pm:182
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> > aptor.pm:249
> > STACK Bio::DB::Persistent::PersistentObject::store
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> > ect.pm:266
> > STACK Bio::DB::BioSQL::AnnotationCollectionAdaptor::store_children
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/AnnotationCollect
> > ionAdaptor.pm:218
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> > aptor.pm:214
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> > aptor.pm:249
> > STACK Bio::DB::Persistent::PersistentObject::store
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> > ect.pm:266
> > STACK Bio::DB::BioSQL::SeqAdaptor::store_children
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/SeqAdaptor.pm:226
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::create
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> > aptor.pm:214
> > STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/BioSQL/BasePersistenceAd
> > aptor.pm:249
> > STACK Bio::DB::Persistent::PersistentObject::store
> > /usr/lib/perl5/site_perl/5.8.0/Bio/DB/Persistent/PersistentObj
> > ect.pm:266
> > STACK (eval) ./load_seqdatabase.pl:437
> > STACK toplevel ./load_seqdatabase.pl:421
> >  
> > --------------------------------------
> > 
> > I cvs'ed the last version of bioperl-db and biosql-schema, so 
> > I'm using the latest version. Is the version that I should be using?
> > 
> > Any hint about what might be the problem?
> > 
> > Thanks in advance,
> > 
> > Albert
> > 
> > _______________________________________________
> > BioSQL-l mailing list
> > BioSQL-l at open-bio.org http://open-bio.org/mailman/listinfo/biosql-l
> > 
>