[BioSQL-l] Adding qualifers to features on a stored sequence
Hilmar Lapp
hlapp@gnf.org
Tue, 22 Oct 2002 00:36:11 -0700
Added test and fixed the problem.
-hilmar
On Monday, October 21, 2002, at 12:07 PM, Hilmar Lapp wrote:
> I think I have an idea what may be going on. The insert statements
> being generated is fine, and them failing is fine too. The problem
> seems to be that the ontology terms for feature source and key
> aren't being looked up upon update. This is a bug. I'll look into
> it and add a test for it. Thanks for reporting. (The temporary
> work-around that I sent earlier should still get around the
> problem.)
>
> -hilmar
>
>> -----Original Message-----
>> From: Tim Henderson [mailto:tjh@alodar.com]
>> Sent: Saturday, October 19, 2002 11:21 PM
>> To: biosql-l@open-bio.org
>> Subject: [BioSQL-l] Adding qualifers to features on a stored sequence
>>
>>
>> I've got a sequence stored in a mysql based BioSQL database,
>> and I want
>> to add a qualifier to one of the features on it.
>>
>> By looking at the code in bioperl-db/t/seqfeature.t I was
>> able to figure
>> out how to add a new feature to an existing sequence; however, when I
>> tried to do a similar thing to add a new qualifier to an existing
>> feature, I got an error. What I tried was this:
>>
>> # Assume these exist
>> my $pseq; # Sequence of interest, fetched from the database.
>> my $cds; # CDS feature on $pseq, got by searching
>> # $pseq->top_SeqFeatures().
>>
>> $cds->add_tag_value('foo', 'This is an added qualifier');
>> $cds->store;
>>
>>
>> I've included the debug output from my script below. The
>> problem seems
>> to be that insert statements are being generated for feature
>> qualifiers
>> that are already in the database. The new qualifier does make it into
>> the database, but the errors leave the feature in an
>> inconsistent state.
>> When I look in the database, its row in the seqfeature table has its
>> ontology_term_id field set to NULL.
>>
>> I'm using the main trunk of bioperl-db. If this is one of
>> those things
>> that is broken for the time being, I'll jury rig something to
>> do what I
>> want by talking directly to the underlying tables. I just
>> wanted to use
>> the BioPerl API if I could.
>>
>>
>> -- Tim
>>
>>
>> attempting to load adaptor class for Bio::Location::Split
>> attempting to load module Bio::DB::BioSQL::SplitAdaptor
>> attempting to load adaptor class for Bio::Location::Atomic
>> attempting to load module Bio::DB::BioSQL::AtomicAdaptor
>> attempting to load adaptor class for Bio::Root::Root
>> attempting to load module Bio::DB::BioSQL::RootAdaptor
>> attempting to load adaptor class for Bio::Root::RootI
>> attempting to load module Bio::DB::BioSQL::RootIAdaptor
>> attempting to load module Bio::DB::BioSQL::RootAdaptor
>> attempting to load adaptor class for Bio::Ontology::Term
>> attempting to load module Bio::DB::BioSQL::TermAdaptor
>> attempting to load adaptor class for Bio::Ontology::Term
>> attempting to load module Bio::DB::BioSQL::TermAdaptor
>> attempting to load adaptor class for Bio::Ontology::Term
>> attempting to load module Bio::DB::BioSQL::TermAdaptor
>> attempting to load adaptor class for Bio::Ontology::Term
>> attempting to load module Bio::DB::BioSQL::TermAdaptor
>> preparing UPDATE statement: UPDATE seqfeature SET
>> seqfeature_rank = ?,
>> bioentry_id = ?, ontology_term_id = ?, seqfeature_source_id = ?
>> WHERE seqfeature_id = ?
>> binding column 1 to "6" (rank)
>> binding column 2 to "1" (FK to bioentry)
>> binding column 3 to "" (FK to ontology_term)
>> binding column 4 to "" (FK to ontology_term)
>> preparing UPDATE statement: UPDATE seqfeature_location SET
>> seq_start =
>> ?, seq_end = ?, seq_strand = ?, location_rank = ?,
>> seqfeature_id = ?
>> WHERE seqfeature_location_id = ?
>> binding column 1 to "796" (start)
>> binding column 2 to "981" (end)
>> binding column 3 to "1" (strand)
>> binding column 4 to "1" (rank)
>> binding column 5 to "6" (FK to seqfeature)
>> binding column 1 to "1589" (start)
>> binding column 2 to "1634" (end)
>> binding column 3 to "1" (strand)
>> binding column 4 to "2" (rank)
>> binding column 5 to "6" (FK to seqfeature)
>> binding column 1 to "1822" (start)
>> binding column 2 to "1869" (end)
>> binding column 3 to "1" (strand)
>> binding column 4 to "3" (rank)
>> binding column 5 to "6" (FK to seqfeature)
>> binding column 1 to "2171" (start)
>> binding column 2 to "2592" (end)
>> binding column 3 to "1" (strand)
>> binding column 4 to "4" (rank)
>> binding column 5 to "6" (FK to seqfeature)
>> attempting to load adaptor class for Bio::Annotation::Collection
>> attempting to load module Bio::DB::BioSQL::CollectionAdaptor
>> attempting to load adaptor class for Bio::Annotation::TypeManager
>> attempting to load module Bio::DB::BioSQL::TypeManagerAdaptor
>> no adaptor found for class Bio::Annotation::TypeManager
>> attempting to load adaptor class for
>> Bio::DB::Persistent::PersistentObjectFactory
>> attempting to load module
>> Bio::DB::BioSQL::PersistentObjectFactoryAdaptor
>> attempting to load adaptor class for Bio::Factory::ObjectFactoryI
>> attempting to load module
>> Bio::DB::BioSQL::ObjectFactoryIAdaptor
>> attempting to load module
>> Bio::DB::BioSQL::ObjectFactoryAdaptor
>> no adaptor found for class
>> Bio::DB::Persistent::PersistentObjectFactory
>> attempting to load driver for adaptor class
>> Bio::DB::BioSQL::AnnotationCollectionAdaptor
>> Using Bio::DB::BioSQL::mysql::AnnotationCollectionAdaptorDriver as
>> driver peer for Bio::DB::BioSQL::AnnotationCollectionAdaptor
>> attempting to load adaptor class for Bio::Ontology::Term
>> attempting to load module Bio::DB::BioSQL::TermAdaptor
>> preparing UK select statement: SELECT ontology_term.ontology_term_id,
>> ontology_term.term_identifier, ontology_term.term_name,
>> ontology_term.term_definition, ontology_term.category_id FROM
>> ontology_term WHERE term_name = ?
>> binding UK column 1 to "Annotation Tags" (name)
>> preparing UK select statement: SELECT ontology_term.ontology_term_id,
>> ontology_term.term_name, NULL, ontology_term.category_id FROM
>> ontology_term WHERE category_id = ? AND term_name = ?
>> binding UK column 1 to "5" (category)
>> binding UK column 2 to "db_xref" (tagname)
>> binding UK column 1 to "5" (category)
>> binding UK column 2 to "codon_start" (tagname)
>> binding UK column 1 to "5" (category)
>> binding UK column 2 to "protein_id" (tagname)
>> binding UK column 1 to "5" (category)
>> binding UK column 2 to "foo" (tagname)
>> preparing INSERT statement: INSERT INTO ontology_term (term_name,
>> category_id) VALUES (?, ?)
>> binding column 1 to "foo" (tagname)
>> binding column 2 to "5" (FK to Bio::Ontology::Term)
>> binding UK column 1 to "5" (category)
>> binding UK column 2 to "translation" (tagname)
>> binding UK column 1 to "5" (category)
>> binding UK column 2 to "product" (tagname)
>> preparing INSERT statement: INSERT INTO seqfeature_qualifier_value
>> (seqfeature_id, ontology_term_id, qualifier_value, qualifier_rank)
>> VALUES (?, ?, ?, ?)
>> binding column 1 to "6" (FK to Bio::SeqFeature::Generic)
>> binding column 2 to "6" (FK to Bio::Annotation::SimpleValue)
>> binding column 3 to "GI:37210" (value)
>> binding column 4 to "1" (rank)
>> DBD::mysql::st execute failed: Duplicate entry '6-6-1' for key 1 at
>> /usr/people/sealsa/bioperl-dev/lib/perl5/site_perl/Bio/DB/BioS
>> QL/BasePersistenceAdaptor.pm
>> line 366.
>> binding column 1 to "6" (FK to Bio::SeqFeature::Generic)
>> binding column 2 to "6" (FK to Bio::Annotation::SimpleValue)
>> binding column 3 to "SWISS-PROT:P01375" (value)
>> binding column 4 to "2" (rank)
>> DBD::mysql::st execute failed: Duplicate entry '6-6-2' for key 1 at
>> /usr/people/sealsa/bioperl-dev/lib/perl5/site_perl/Bio/DB/BioS
>> QL/BasePersistenceAdaptor.pm
>> line 366.
>> binding column 1 to "6" (FK to Bio::SeqFeature::Generic)
>> binding column 2 to "17" (FK to Bio::Annotation::SimpleValue)
>> binding column 3 to "1" (value)
>> binding column 4 to "1" (rank)
>> DBD::mysql::st execute failed: Duplicate entry '6-17-1' for key 1 at
>> /usr/people/sealsa/bioperl-dev/lib/perl5/site_perl/Bio/DB/BioS
>> QL/BasePersistenceAdaptor.pm
>> line 366.
>> binding column 1 to "6" (FK to Bio::SeqFeature::Generic)
>> binding column 2 to "18" (FK to Bio::Annotation::SimpleValue)
>> binding column 3 to "CAA26669.1" (value)
>> binding column 4 to "1" (rank)
>> DBD::mysql::st execute failed: Duplicate entry '6-18-1' for key 1 at
>> /usr/people/sealsa/bioperl-dev/lib/perl5/site_perl/Bio/DB/BioS
>> QL/BasePersistenceAdaptor.pm
>> line 366.
>> binding UK column 1 to "5" (category)
>> binding UK column 2 to "foo" (tagname)
>> binding column 1 to "6" (FK to Bio::SeqFeature::Generic)
>> binding column 2 to "27" (FK to Bio::Annotation::SimpleValue)
>> binding column 3 to "This is an added qualifier" (value)
>> binding column 4 to "1" (rank)
>> binding column 1 to "6" (FK to Bio::SeqFeature::Generic)
>> binding column 2 to "20" (FK to Bio::Annotation::SimpleValue)
>> binding column 3 to
>> "MSTESMIRDVELAEEALPKKTGGPQGSRRCLFLSLFSFLIVAGATTLFCLLHFGVIGPQRE
>> EFPRDLSLISPLAQAVRSSSRTPSDKPVAHVVANPQAEGQLQWLNRRANALLANGVELRDNQ
>> LVVPSEGLYLIYSQVLFKGQGCPSTHVLLTHTISRIAVSYQTKVNLLSAIKSPCQRETPEGA
>> EAKPWYEPIYLGGVFQLEKGDRLSAEINRPDYLDFAESGQVYFGIIAL"
>> (value)
>> binding column 4 to "1" (rank)
>> DBD::mysql::st execute failed: Duplicate entry '6-20-1' for key 1 at
>> /usr/people/sealsa/bioperl-dev/lib/perl5/site_perl/Bio/DB/BioS
>> QL/BasePersistenceAdaptor.pm
>> line 366.
>> binding column 1 to "6" (FK to Bio::SeqFeature::Generic)
>> binding column 2 to "19" (FK to Bio::Annotation::SimpleValue)
>> binding column 3 to "TNF-alpha" (value)
>> binding column 4 to "1" (rank)
>> DBD::mysql::st execute failed: Duplicate entry '6-19-1' for key 1 at
>> /usr/people/sealsa/bioperl-dev/lib/perl5/site_perl/Bio/DB/BioS
>> QL/BasePersistenceAdaptor.pm
>> line 366.
>>
>> ------------- EXCEPTION -------------
>> MSG: failed to store one or more child objects for an
>> instance of class
>> Bio::SeqFeature::Generic (PK=6)
>> STACK Bio::Root::RootI::warn
>> /usr/people/sealsa/bioperl-dev/lib/perl5/site_perl/Bio/Root/Ro
>> otI.pm:182
>> STACK Bio::DB::BioSQL::BasePersistenceAdaptor::store
>> /usr/people/sealsa/bioperl-dev/lib/perl5/site_perl/Bio/DB/BioS
>> QL/BasePersistenceAdaptor.pm:237
>> STACK Bio::DB::Persistent::PersistentObject::store
>> /usr/people/sealsa/bioperl-dev/lib/perl5/site_perl/Bio/DB/Pers
>> istent/PersistentObject.pm:266
>> STACK (eval) ./add_feat_qual.pl:101
>> STACK toplevel ./add_feat_qual.pl:100
>>
>> --------------------------------------
>>
>>
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--
-------------------------------------------------------------
Hilmar Lapp email: lapp at gnf.org
GNF, San Diego, Ca. 92121 phone: +1-858-812-1757
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