[Bioperl-l] Fwd: problem with bioperl (where's the Mus?)

Anand C. Patel acpatel at gmail.com
Sat Aug 22 22:44:20 UTC 2009


On Aug 22, 2009, at 4:36 PM, Hilmar Lapp wrote:

> That's a pretty strange bug. Anand, which version of BioPerl and  
> Bioperl-db are you running?

BioPerl is:
https://launchpad.net/ubuntu/karmic/+source/bioperl/1.6.0-2ubuntu1
(1.6.0 loaded via apt-get into ubuntu karmic alpha 4)

BioPerl-db is version 1.006 (1.6.0) loaded via CPAN.

BioSQL is 1.0.1

I think I know what's broken.  Using load_seqdatabases.pl, I'd put a  
set of sequences from genbank into a biosql db in mysql.

I'd also loaded the ncbi taxonomy using the load_ncbi_taxonomy.pl  
script from biosql.

When I searched for house (as in house mouse), I found that the name  
of the type of taxon class was "genbank common name".

When I searched for musculus, it does appear as a type of "scientific  
name".

> Note that the genus *is* actually there in the lineage (and hence  
> does get retrieved from the database). Apparently the Species object  
> fails to pull it out correctly, though?
>
> Anand - I suspect there have been some warnings printed to the  
> terminal - can you post these, and otherwise confirm that there  
> haven't been any?
>
> 	-hilmar

I'm not just getting warnings.  I'm getting errors.  Tons of them.   
It's a wonder it's working at all.

I started with the getentry.cgi script in the cgi-bin folder, and  
stripped most of it away.

Code:
#!/usr/bin/perl

use DBI;
use CGI::Carp qw( fatalsToBrowser );
use CGI qw/:standard/;
use Bio::DB::BioDB;
use Bio::Seq::RichSeq;
use Bio::SeqIO;
use IO::String;

my $q = new CGI;                        # create new CGI object
print $q->header;                    # create the HTTP header

my $value = "NM_017474";

my $host   = "localhost";
my $dbname = "biosql";
my $driver = "mysql";
my $dbuser = "webuser";
my $dbpass = "wrjFfjjW9y243xvF";

my $biodbname = "genbank";

my $seq;

eval {

     my $db = Bio::DB::BioDB->new(-database => "biosql",
				 -host     => $host,
				 -dbname   => $dbname,
				 -driver   => $driver,
				 -user     => $dbuser,
				 -pass     => $dbpass,
				 -verbose  => 10,
				 );

     my $seqadaptor = $db->get_object_adaptor('Bio::SeqI');

     $seq = Bio::Seq::RichSeq->new( -accession_number => $value, - 
namespace => $biodbname );

     $seq = $seqadaptor->find_by_unique_key($seq);
};

my $seqfh = IO::String->new($gbstring);
my $ioseq = Bio::SeqIO->new(-fh => $seqfh, -format => 'genbank');
$ioseq->write_seq($seq);


if( $@ || !defined $seq) {
     print "Got fetch exception of...\n<pre>$@\n</pre>";
     exit(0);
}

print "<title>BioSQL display of ". $seq->display_id ."</title>\n";
print "<body>\n";

print "<HR>\n<pre>".$gbstring."\n</pre>\n<br>\n</body>";

Errors (some but not all):
  test1.cgi: attempting to load adaptor class for Bio::SeqI
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::SeqIAdaptor
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::SeqAdaptor
  test1.cgi: instantiating adaptor class Bio::DB::BioSQL::SeqAdaptor
  test1.cgi: attempting to load adaptor class for BioNamespace
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::BioNamespaceAdaptor
  test1.cgi: instantiating adaptor class  
Bio::DB::BioSQL::BioNamespaceAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BioNamespaceAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BasePersistenceAdaptor
  test1.cgi: Using  
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver peer  
for Bio::DB::BioSQL::BioNamespaceAdaptor
  test1.cgi: preparing UK select statement: SELECT  
biodatabase.biodatabase_id, biodatabase.name, biodatabase.authority  
FROM biodatabase WHERE name = ?
  test1.cgi: BioNamespaceAdaptor: binding UK column 1 to  
"genbank" (namespace)
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::SeqAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::PrimarySeqAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BasePersistenceAdaptor
  test1.cgi: Using  
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver peer  
for Bio::DB::BioSQL::SeqAdaptor
  test1.cgi: preparing UK select statement: SELECT  
bioentry.bioentry_id, bioentry.name, bioentry.identifier,  
bioentry.accession, bioentry.description, bioentry.version,  
bioentry.division, bioentry.biodatabase_id, bioentry.taxon_id FROM  
bioentry WHERE biodatabase_id = ? AND accession = ?
  test1.cgi: SeqAdaptor: binding UK column 1 to "1" (bionamespace)
  test1.cgi: SeqAdaptor: binding UK column 2 to  
"NM_017474" (accession_number)
  test1.cgi: attempting to load adaptor class for Bio::PrimarySeq
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::PrimarySeqAdaptor
  test1.cgi: instantiating adaptor class  
Bio::DB::BioSQL::PrimarySeqAdaptor
  test1.cgi: preparing PK select statement: SELECT  
biodatabase.biodatabase_id, biodatabase.name, biodatabase.authority  
FROM biodatabase WHERE biodatabase_id = ?
  test1.cgi: BioNamespaceAdaptor: binding PK column to "1"
  test1.cgi: attempting to load adaptor class for Bio::Species
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::SpeciesAdaptor
  test1.cgi: instantiating adaptor class Bio::DB::BioSQL::SpeciesAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::SpeciesAdaptor
  test1.cgi: Using Bio::DB::BioSQL::mysql::SpeciesAdaptorDriver as  
driver peer for Bio::DB::BioSQL::SpeciesAdaptor
  test1.cgi: preparing PK select statement: SELECT  
taxon_name.taxon_id, NULL, NULL, taxon.ncbi_taxon_id, taxon_name.name,  
NULL FROM taxon, taxon_name WHERE taxon.taxon_id = taxon_name.taxon_id  
AND taxon_name.name_class = 'scientific name' AND taxon.taxon_id = ?
  test1.cgi: SpeciesAdaptor: binding PK column to "138"
  test1.cgi: prepare SELECT CLASSIFICATION: SELECT name.name,  
node.node_rank FROM taxon node, taxon taxon, taxon_name name WHERE  
name.taxon_id = node.taxon_id AND taxon.left_value >= node.left_value  
AND taxon.left_value <= node.right_value AND taxon.taxon_id = ? AND  
name.name_class = 'scientific name' ORDER BY node.left_value
  test1.cgi: preparing SELECT COMMON_NAME: SELECT taxon_name.name FROM  
taxon_name WHERE taxon_name.taxon_id = ? AND taxon_name.name_class =  
'common_name'
  test1.cgi: attempting to load adaptor class for Bio::Tree::Tree
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::TreeAdaptor
  test1.cgi: attempting to load adaptor class for Bio::Root::Root
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::RootAdaptor
  test1.cgi: attempting to load adaptor class for Bio::Root::RootI
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::RootIAdaptor
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::RootAdaptor
  test1.cgi: attempting to load adaptor class for Bio::Tree::TreeI
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::TreeIAdaptor
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::TreeAdaptor
  test1.cgi: attempting to load adaptor class for  
Bio::Tree::TreeFunctionsI
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::TreeFunctionsIAdaptor
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::TreeFunctionsAdaptor
  test1.cgi: no adaptor found for class Bio::Tree::Tree
  test1.cgi: attempting to load adaptor class for  
Bio::DB::Taxonomy::list
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::listAdaptor
  test1.cgi: attempting to load adaptor class for Bio::DB::Taxonomy
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::TaxonomyAdaptor
  test1.cgi: no adaptor found for class Bio::DB::Taxonomy::list
  test1.cgi: attempting to load adaptor class for Biosequence
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::BiosequenceAdaptor
  test1.cgi: instantiating adaptor class  
Bio::DB::BioSQL::BiosequenceAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BiosequenceAdaptor
  test1.cgi: Using Bio::DB::BioSQL::mysql::BiosequenceAdaptorDriver as  
driver peer for Bio::DB::BioSQL::BiosequenceAdaptor
  test1.cgi: preparing UK select statement: SELECT  
biosequence.bioentry_id, biosequence.version, biosequence.length,  
biosequence.alphabet, NULL, NULL, biosequence.bioentry_id FROM  
biosequence WHERE bioentry_id = ?
  test1.cgi: BiosequenceAdaptor: binding UK column 1 to  
"1" (primary_seq)
  test1.cgi: attempting to load adaptor class for  
Bio::AnnotationCollectionI
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::AnnotationCollectionIAdaptor
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::AnnotationCollectionAdaptor
  test1.cgi: instantiating adaptor class  
Bio::DB::BioSQL::AnnotationCollectionAdaptor
  test1.cgi: attempting to load adaptor class for  
Bio::Annotation::TypeManager
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::TypeManagerAdaptor
  test1.cgi: no adaptor found for class Bio::Annotation::TypeManager
  test1.cgi: attempting to load adaptor class for  
Bio::Annotation::Reference
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::ReferenceAdaptor
  test1.cgi: instantiating adaptor class  
Bio::DB::BioSQL::ReferenceAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::ReferenceAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BasePersistenceAdaptor
  test1.cgi: Using  
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver peer  
for Bio::DB::BioSQL::ReferenceAdaptor
  test1.cgi: preparing SELECT ASSOC query: SELECT t2.reference_id,  
t2.authors, t2.title, t2.location, t2.crc,  
bioentry_reference.start_pos, bioentry_reference.end_pos,  
bioentry_reference.rank, t2.dbxref_id FROM bioentry t1, reference t2,  
bioentry_reference WHERE t1.bioentry_id =  
bioentry_reference.bioentry_id AND t2.reference_id =  
bioentry_reference.reference_id AND t1.bioentry_id = ?
  test1.cgi: ReferenceAdaptor: binding ASSOC column 1 to "1" (FK to  
Bio::Seq::RichSeq)
  test1.cgi: attempting to load adaptor class for  
Bio::Annotation::DBLink
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::DBLinkAdaptor
  test1.cgi: instantiating adaptor class Bio::DB::BioSQL::DBLinkAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::DBLinkAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BasePersistenceAdaptor
  test1.cgi: Using  
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver peer  
for Bio::DB::BioSQL::DBLinkAdaptor
  test1.cgi: preparing PK select statement: SELECT dbxref.dbxref_id,  
dbxref.dbname, dbxref.accession, dbxref.version, NULL FROM dbxref  
WHERE dbxref_id = ?
  test1.cgi: DBLinkAdaptor: binding PK column to "1"
  test1.cgi: DBLinkAdaptor: binding PK column to "2"
  test1.cgi: DBLinkAdaptor: binding PK column to "3"
  test1.cgi: DBLinkAdaptor: binding PK column to "4"
  test1.cgi: DBLinkAdaptor: binding PK column to "5"
  test1.cgi: DBLinkAdaptor: binding PK column to "6"
  test1.cgi: DBLinkAdaptor: binding PK column to "7"
  test1.cgi: DBLinkAdaptor: binding PK column to "8"
  test1.cgi: DBLinkAdaptor: binding PK column to "9"
  test1.cgi: DBLinkAdaptor: binding PK column to "10"
  test1.cgi: preparing SELECT ASSOC query: SELECT t2.dbxref_id,  
t2.dbname, t2.accession, t2.version, bioentry_dbxref.rank FROM  
bioentry t1, dbxref t2, bioentry_dbxref WHERE t1.bioentry_id =  
bioentry_dbxref.bioentry_id AND t2.dbxref_id =  
bioentry_dbxref.dbxref_id AND t1.bioentry_id = ?
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "1" (FK to  
Bio::Seq::RichSeq)
  test1.cgi: attempting to load adaptor class for  
Bio::Annotation::SimpleValue
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::SimpleValueAdaptor
  test1.cgi: instantiating adaptor class  
Bio::DB::BioSQL::SimpleValueAdaptor
  test1.cgi: attempting to load adaptor class for  
Bio::Ontology::Ontology
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::OntologyAdaptor
  test1.cgi: instantiating adaptor class  
Bio::DB::BioSQL::OntologyAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::OntologyAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BasePersistenceAdaptor
  test1.cgi: Using  
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver peer  
for Bio::DB::BioSQL::OntologyAdaptor
  test1.cgi: preparing UK select statement: SELECT  
ontology.ontology_id, ontology.name, ontology.definition FROM ontology  
WHERE name = ?
  test1.cgi: OntologyAdaptor: binding UK column 1 to "Annotation  
Tags" (name)
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::SimpleValueAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::TermAdaptor
  test1.cgi: Using Bio::DB::BioSQL::mysql::TermAdaptorDriver as driver  
peer for Bio::DB::BioSQL::SimpleValueAdaptor
  test1.cgi: preparing SELECT ASSOC query: SELECT t2.term_id, t2.name,  
bioentry_qualifier_value.value, bioentry_qualifier_value.rank,  
t2.ontology_id FROM bioentry t1, term t2, bioentry_qualifier_value  
WHERE t1.bioentry_id = bioentry_qualifier_value.bioentry_id AND  
t2.term_id = bioentry_qualifier_value.term_id AND (t1.bioentry_id = ?  
AND t2.ontology_id = ?)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 1 to "1" (FK to  
Bio::Seq::RichSeq)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 2 to  
"31" (constraint Bio::Annotation::SimpleValue::ontology)
  test1.cgi: attempting to load adaptor class for  
Bio::Annotation::OntologyTerm
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::OntologyTermAdaptor
  test1.cgi: attempting to load adaptor class for Bio::AnnotationI
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::AnnotationIAdaptor
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::AnnotationAdaptor
  test1.cgi: attempting to load adaptor class for Bio::Ontology::TermI
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::TermIAdaptor
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::TermAdaptor
  test1.cgi: instantiating adaptor class Bio::DB::BioSQL::TermAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::TermAdaptor
  test1.cgi: Using Bio::DB::BioSQL::mysql::TermAdaptorDriver as driver  
peer for Bio::DB::BioSQL::TermAdaptor
  test1.cgi: preparing SELECT ASSOC query: SELECT t2.term_id,  
t2.identifier, t2.name, t2.definition, t2.is_obsolete,  
bioentry_qualifier_value.rank, t2.ontology_id FROM bioentry t1, term  
t2, bioentry_qualifier_value WHERE t1.bioentry_id =  
bioentry_qualifier_value.bioentry_id AND t2.term_id =  
bioentry_qualifier_value.term_id AND (t1.bioentry_id = ? AND  
t2.ontology_id != ?)
  test1.cgi: TermAdaptor: binding ASSOC column 1 to "1" (FK to  
Bio::Seq::RichSeq)
  test1.cgi: TermAdaptor: binding ASSOC column 2 to "31" (constraint  
Bio::Annotation::OntologyTerm::ontology)
  test1.cgi: attempting to load adaptor class for  
Bio::Annotation::Comment
  test1.cgi: \tattempting to load module Bio::DB::BioSQL::CommentAdaptor
  test1.cgi: instantiating adaptor class Bio::DB::BioSQL::CommentAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::CommentAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BasePersistenceAdaptor
  test1.cgi: Using  
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver peer  
for Bio::DB::BioSQL::CommentAdaptor
  test1.cgi: preparing query: SELECT t1.comment_id, t1.comment_text,  
t1.rank, t1.bioentry_id FROM comment t1 WHERE t1.bioentry_id = ?
  test1.cgi: Query FIND Bio::Annotation::Comment BY Bio::Seq::RichSeq:  
binding column 1 to "1"
  test1.cgi: attempting to load adaptor class for Bio::SeqFeatureI
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::SeqFeatureIAdaptor
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::SeqFeatureAdaptor
  test1.cgi: instantiating adaptor class  
Bio::DB::BioSQL::SeqFeatureAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::SeqFeatureAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BasePersistenceAdaptor
  test1.cgi: Using  
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver peer  
for Bio::DB::BioSQL::SeqFeatureAdaptor
  test1.cgi: preparing query: SELECT t1.seqfeature_id,  
t1.display_name, t1.rank, t1.bioentry_id, t1.type_term_id,  
t1.source_term_id FROM seqfeature t1 WHERE t1.bioentry_id = ? ORDER BY  
t1.rank
  test1.cgi: Query FIND FEATURE BY SEQ: binding column 1 to "1"
  test1.cgi: preparing PK select statement: SELECT term.term_id,  
term.identifier, term.name, term.definition, term.is_obsolete, NULL,  
term.ontology_id FROM term WHERE term_id = ?
  test1.cgi: TermAdaptor: binding PK column to "245"
  test1.cgi: attempting to load adaptor class for  
Bio::Ontology::OntologyI
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::OntologyIAdaptor
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::OntologyAdaptor
  test1.cgi: preparing PK select statement: SELECT  
ontology.ontology_id, ontology.name, ontology.definition FROM ontology  
WHERE ontology_id = ?
  test1.cgi: OntologyAdaptor: binding PK column to "32"
  test1.cgi: preparing SELECT ASSOC query: SELECT t2.dbxref_id,  
t2.dbname, t2.accession, t2.version, term_dbxref.rank FROM term t1,  
dbxref t2, term_dbxref WHERE t1.term_id = term_dbxref.term_id AND  
t2.dbxref_id = term_dbxref.dbxref_id AND t1.term_id = ?
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "245" (FK to  
Bio::Ontology::Term)
  test1.cgi: SELECT SYNONYMS: preparing: SELECT synonym FROM  
term_synonym WHERE term_id = ?
  test1.cgi: SELECT SYNONYMS: executing with values (245) (FK to  
Bio::Ontology::Term)
  test1.cgi: TermAdaptor: binding PK column to "246"
  test1.cgi: OntologyAdaptor: binding PK column to "33"
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "246" (FK to  
Bio::Ontology::Term)
  test1.cgi: SELECT SYNONYMS: executing with values (246) (FK to  
Bio::Ontology::Term)
  test1.cgi: attempting to load adaptor class for Bio::LocationI
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::LocationIAdaptor
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::LocationAdaptor
  test1.cgi: instantiating adaptor class  
Bio::DB::BioSQL::LocationAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::LocationAdaptor
  test1.cgi: attempting to load driver for adaptor class  
Bio::DB::BioSQL::BasePersistenceAdaptor
  test1.cgi: Using  
Bio::DB::BioSQL::mysql::BasePersistenceAdaptorDriver as driver peer  
for Bio::DB::BioSQL::LocationAdaptor
  test1.cgi: preparing query: SELECT t1.location_id, t1.start_pos,  
t1.end_pos, t1.strand, t1.rank, t1.seqfeature_id, t1.dbxref_id FROM  
location t1 WHERE t1.seqfeature_id = ?
  test1.cgi: Query FIND LOCATION BY FEATURE: binding column 1 to "1"
  test1.cgi: attempting to load adaptor class for  
Bio::DB::Persistent::PersistentObjectFactory
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::PersistentObjectFactoryAdaptor
  test1.cgi: attempting to load adaptor class for  
Bio::Factory::ObjectFactoryI
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::ObjectFactoryIAdaptor
  test1.cgi: \tattempting to load module  
Bio::DB::BioSQL::ObjectFactoryAdaptor
  test1.cgi: no adaptor found for class  
Bio::DB::Persistent::PersistentObjectFactory
  test1.cgi: preparing SELECT ASSOC query: SELECT t2.dbxref_id,  
t2.dbname, t2.accession, t2.version, seqfeature_dbxref.rank FROM  
seqfeature t1, dbxref t2, seqfeature_dbxref WHERE t1.seqfeature_id =  
seqfeature_dbxref.seqfeature_id AND t2.dbxref_id =  
seqfeature_dbxref.dbxref_id AND t1.seqfeature_id = ?
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "1" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: preparing SELECT ASSOC query: SELECT t2.term_id, t2.name,  
seqfeature_qualifier_value.value, seqfeature_qualifier_value.rank,  
t2.ontology_id FROM seqfeature t1, term t2, seqfeature_qualifier_value  
WHERE t1.seqfeature_id = seqfeature_qualifier_value.seqfeature_id AND  
t2.term_id = seqfeature_qualifier_value.term_id AND (t1.seqfeature_id  
= ? AND t2.ontology_id = ?)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 1 to "1" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 2 to  
"31" (constraint Bio::Annotation::SimpleValue::ontology)
  test1.cgi: preparing SELECT ASSOC query: SELECT t2.term_id,  
t2.identifier, t2.name, t2.definition, t2.is_obsolete,  
seqfeature_qualifier_value.rank, t2.ontology_id FROM seqfeature t1,  
term t2, seqfeature_qualifier_value WHERE t1.seqfeature_id =  
seqfeature_qualifier_value.seqfeature_id AND t2.term_id =  
seqfeature_qualifier_value.term_id AND (t1.seqfeature_id = ? AND  
t2.ontology_id != ?)
  test1.cgi: TermAdaptor: binding ASSOC column 1 to "1" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: TermAdaptor: binding ASSOC column 2 to "31" (constraint  
Bio::Annotation::OntologyTerm::ontology)
  test1.cgi: preparing query: SELECT t1.comment_id, t1.comment_text,  
t1.rank, t1.bioentry_id FROM comment t1 WHERE 1 = 1
  test1.cgi: Query FIND Bio::Annotation::Comment BY  
Bio::SeqFeature::Generic: binding column 1 to "1"
  test1.cgi: TermAdaptor: binding PK column to "260"
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "260" (FK to  
Bio::Ontology::Term)
  test1.cgi: SELECT SYNONYMS: executing with values (260) (FK to  
Bio::Ontology::Term)
  test1.cgi: Query FIND LOCATION BY FEATURE: binding column 1 to "2"
  test1.cgi: no adaptor found for class  
Bio::DB::Persistent::PersistentObjectFactory
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "2" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 1 to "2" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 2 to  
"31" (constraint Bio::Annotation::SimpleValue::ontology)
  test1.cgi: TermAdaptor: binding ASSOC column 1 to "2" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: TermAdaptor: binding ASSOC column 2 to "31" (constraint  
Bio::Annotation::OntologyTerm::ontology)
  test1.cgi: TermAdaptor: binding PK column to "250"
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "250" (FK to  
Bio::Ontology::Term)
  test1.cgi: SELECT SYNONYMS: executing with values (250) (FK to  
Bio::Ontology::Term)
  test1.cgi: Query FIND LOCATION BY FEATURE: binding column 1 to "3"
  test1.cgi: no adaptor found for class  
Bio::DB::Persistent::PersistentObjectFactory
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "3" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 1 to "3" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 2 to  
"31" (constraint Bio::Annotation::SimpleValue::ontology)
  test1.cgi: TermAdaptor: binding ASSOC column 1 to "3" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: TermAdaptor: binding ASSOC column 2 to "31" (constraint  
Bio::Annotation::OntologyTerm::ontology)
  test1.cgi: TermAdaptor: binding PK column to "264"
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "264" (FK to  
Bio::Ontology::Term)
  test1.cgi: SELECT SYNONYMS: executing with values (264) (FK to  
Bio::Ontology::Term)
  test1.cgi: Query FIND LOCATION BY FEATURE: binding column 1 to "4"
  test1.cgi: no adaptor found for class  
Bio::DB::Persistent::PersistentObjectFactory
  test1.cgi: DBLinkAdaptor: binding ASSOC column 1 to "4" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 1 to "4" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: SimpleValueAdaptor: binding ASSOC column 2 to  
"31" (constraint Bio::Annotation::SimpleValue::ontology)
  test1.cgi: TermAdaptor: binding ASSOC column 1 to "4" (FK to  
Bio::SeqFeature::Generic)
  test1.cgi: TermAdaptor: binding ASSOC column 2 to "31" (constraint  
Bio::Annotation::OntologyTerm::ontology)
  test1.cgi: preparing SELECT statement: SELECT seq FROM biosequence  
WHERE bioentry_id = ?


>
> On Aug 22, 2009, at 4:17 PM, Chris Fields wrote:
>
>> Anand,
>>
>> You should always post emails to the bioperl-l mailing list, never  
>> to individual developers (you'll get an answer much faster).  Keep  
>> responses on the list as well.
>>
>> Though I use bioperl-db some, I'm probably not the best person to  
>> ask.  Does anyone know what's going on with this?  Does this have  
>> to do with the Species/Taxon refactoring?
>>
>> chris
>>
>> Begin forwarded message:
>>
>>> From: "Anand C. Patel" <acpatel at gmail.com>
>>> Date: August 22, 2009 2:57:42 PM CDT
>>> To: cjfields at illinois.edu
>>> Subject: problem with bioperl (where's the Mus?)
>>>
>>> Dr. Fields,
>>>
>>> I'm struggling with what seems to be a strange quirk in Bioperl  
>>> +/- Bioperl-db/BioSQL.
>>>
>>> I've successfully loaded in genbank sequences into a biosql  
>>> database.
>>>
>>> When I try to write a genbank sequence back out, a curious thing  
>>> happens -- the Genus is missing from the SOURCE and ORGANISM areas.
>>>
>>> Despite reporting:
>>> primary tag: source
>>> tag: chromosome
>>>  value: 3
>>>
>>> tag: db_xref
>>>  value: taxon:10090
>>>
>>> tag: map
>>>  value: 3 74.5 cM
>>>
>>> tag: mol_type
>>>  value: mRNA
>>>
>>> tag: organism
>>>  value: Mus musculus
>>> The sequence when printed out via SeqIO looks like this:
>>> LOCUS       NM_017474               2935 bp    dna     linear    
>>> ROD 13-AUG-2009
>>> DEFINITION  Mus musculus chloride channel calcium activated 3  
>>> (Clca3), mRNA.
>>> ACCESSION   NM_017474 XM_978159
>>> VERSION     NM_017474.2  GI:255918210
>>> KEYWORDS    .
>>> SOURCE      musculus
>>> ORGANISM  musculus
>>>          Eukaryota; Fungi/Metazoa group; Metazoa; Eumetazoa;  
>>> Bilateria;
>>>          Coelomata; Deuterostomia; Chordata; Craniata; Vertebrata;
>>>          Gnathostomata; Teleostomi; Euteleostomi; Sarcopterygii;  
>>> Tetrapoda;
>>>          Amniota; Mammalia; Theria; Eutheria; Euarchontoglires;  
>>> Glires;
>>>          Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus.
>>> Confession -- I have a final project due Monday wherein I boldly  
>>> elected to interface Bioperl, MySQL, Perl, and CGI.
>>> (I'm an MD getting my MS in Bioinformatics.)
>>> After many misadventures, I'm getting to the point where I could  
>>> actually complete the objectives, but this is bug is rather  
>>> problematic.
>>> Thanks,
>>> Anand
>>> Anand C. Patel, MD
>>> Assistant Professor of Pediatrics
>>> Division of Allergy/Pulmonary Medicine
>>> Department of Pediatrics
>>> Washington University School of Medicine
>>> 660 South Euclid Ave, Campus Box 8052
>>> St. Louis, MO 63110
>>> acpatel at wustl.edu
>>> acpatel at gmail.com
>>> acpatel at jhu.edu
>>>
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
> -- 
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
>
>
>




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