From soumyadeep_nandi at yahoo.com Mon Dec 5 04:38:46 2005 From: soumyadeep_nandi at yahoo.com (Soumyadeep nandi) Date: Mon Dec 5 04:43:02 2005 Subject: [BioSQL-l] problem loading swissprot sequences into bioperl-db. Message-ID: <20051205093846.54647.qmail@web52213.mail.yahoo.com> 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@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 --------------------------------- Yahoo! Personals Let fate take it's course directly to your email. See who's waiting for you Yahoo! Personals From hlapp at gnf.org Mon Dec 5 11:32:35 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Mon Dec 5 11:39:27 2005 Subject: [BioSQL-l] problem loading swissprot sequences into bioperl-db. In-Reply-To: <20051205093846.54647.qmail@web52213.mail.yahoo.com> References: <20051205093846.54647.qmail@web52213.mail.yahoo.com> Message-ID: 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@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 > > > > > --------------------------------- > Yahoo! Personals > Let fate take it's course directly to your email. > See who's waiting for you Yahoo! Personals > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 ------------------------------------------------------------- From soumyadeep_nandi at yahoo.com Wed Dec 7 08:06:09 2005 From: soumyadeep_nandi at yahoo.com (Soumyadeep nandi) Date: Wed Dec 7 08:03:40 2005 Subject: [BioSQL-l] problem loading swissprot sequences into bioperl-db. In-Reply-To: Message-ID: <20051207130610.71317.qmail@web52213.mail.yahoo.com> 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: 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@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 > > > > > --------------------------------- > Yahoo! Personals > Let fate take it's course directly to your email. > See who's waiting for you Yahoo! Personals > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- 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 From hlapp at gnf.org Wed Dec 7 14:53:46 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Dec 7 14:55:41 2005 Subject: [BioSQL-l] problem loading swissprot sequences into bioperl-db. In-Reply-To: <20051207130610.71317.qmail@web52213.mail.yahoo.com> References: <20051207130610.71317.qmail@web52213.mail.yahoo.com> Message-ID: <356eb2af088d76168f117c6482590087@gnf.org> 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@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 >> > >> > >> > >> > >> > --------------------------------- >> > Yahoo! Personals >> > Let fate take it's course directly to your email. >> > See who's waiting for you Yahoo! Personals >> > _______________________________________________ >> > BioSQL-l mailing list >> > BioSQL-l@open-bio.org >> > http://open-bio.org/mailman/listinfo/biosql-l >> > >> -- >> ------------------------------------------------------------- >> 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 ------------------------------------------------------------- From angshu96 at gmail.com Thu Dec 8 11:00:48 2005 From: angshu96 at gmail.com (Angshu Kar) Date: Thu Dec 8 20:01:00 2005 Subject: [BioSQL-l] Uploading data to biosql dbs Message-ID: Hi, I've created 5 tables (taxon, taxon name, bioentry, biosequence, biodatabase) in my postgresql database (linux box) using the biosql schema ddl from http://cvs.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/biosql-schema/sql/biosqldb-pg.sql?rev=1.29&cvsroot=biosql&content-type=text/vnd.viewcvs-markup . Now I want to load the tables with arabidopsis data (say from tigr db). Could you please let me know where can I find such scripts for pgsql? And also I find at http://bio.perl.org/Core/Latest/index.shtml that the DB module has not been updated since 2001. Do I need to install that? Or are there some new releases? I'll be obliged if you can guide. Thanks, Angshu From soumyadeep_nandi at yahoo.com Thu Dec 8 22:42:05 2005 From: soumyadeep_nandi at yahoo.com (Soumyadeep nandi) Date: Thu Dec 8 22:48:52 2005 Subject: [BioSQL-l] problem loading swissprot sequences into bioperl-db. In-Reply-To: <356eb2af088d76168f117c6482590087@gnf.org> Message-ID: <20051209034205.23089.qmail@web52209.mail.yahoo.com> 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 () 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 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@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 >> > >> > >> > >> > >> > --------------------------------- >> > Yahoo! Personals >> > Let fate take it's course directly to your email. >> > See who's waiting for you Yahoo! Personals >> > _______________________________________________ >> > BioSQL-l mailing list >> > BioSQL-l@open-bio.org >> > http://open-bio.org/mailman/listinfo/biosql-l >> > >> -- >> ------------------------------------------------------------- >> 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 ------------------------------------------------------------- --------------------------------- Yahoo! Shopping Find Great Deals on Holiday Gifts at Yahoo! Shopping From mark.schreiber at novartis.com Wed Dec 14 00:29:46 2005 From: mark.schreiber at novartis.com (mark.schreiber@novartis.com) Date: Wed Dec 14 00:33:56 2005 Subject: [BioSQL-l] entrez gene into biosql Message-ID: Hello - Has any one ever tried to squeeze Entrez gene records into BioSQL? Was it successful? What mappings did you use? Thanks, - Mark Mark Schreiber Research Investigator (Bioinformatics) Novartis Institute for Tropical Diseases (NITD) 10 Biopolis Road #05-01 Chromos Singapore 138670 www.nitd.novartis.com phone +65 6722 2973 fax +65 6722 2910 From hlapp at gnf.org Wed Dec 14 00:47:50 2005 From: hlapp at gnf.org (Hilmar Lapp) Date: Wed Dec 14 00:45:08 2005 Subject: [BioSQL-l] entrez gene into biosql In-Reply-To: References: Message-ID: Bioperl has an EntrezGene SeqIO parser, so load_seqdatabase.pl should be able to load it. What I still haven't gotten to, however, is to validate that the resulting data structure is compatible with the one created by the SeqIO::locuslink parser. I.e., the mappings ought to be very similar, in spirit where the annotation didn't exist in LL, and literally where the annotation was also present in the LL format. The validation I was referring foremost pertains to the SeqIO parser, as without further customary processing that will pretty much determine the resulting structure in BioSQL. As a start, you can load the old LL download into BioSQL and see where things go. (Pretty straightforward - most of the tags end up as annotation.) -hilmar On Dec 13, 2005, at 9:29 PM, mark.schreiber@novartis.com wrote: > Hello - > > Has any one ever tried to squeeze Entrez gene records into BioSQL? Was > it > successful? What mappings did you use? > > Thanks, > > - Mark > > Mark Schreiber > Research Investigator (Bioinformatics) > > Novartis Institute for Tropical Diseases (NITD) > 10 Biopolis Road > #05-01 Chromos > Singapore 138670 > www.nitd.novartis.com > > phone +65 6722 2973 > fax +65 6722 2910 > > _______________________________________________ > BioSQL-l mailing list > BioSQL-l@open-bio.org > http://open-bio.org/mailman/listinfo/biosql-l > -- ------------------------------------------------------------- Hilmar Lapp email: lapp at gnf.org GNF, San Diego, Ca. 92121 phone: +1-858-812-1757 -------------------------------------------------------------