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

[Hilmar Lapp]

Do not use Bioperl-db-0.1 unless you are prepared to also use a very 
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 our 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 from 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
-------------------------------------------------------------