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

[Soumyadeep nandi]

 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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