[Bioperl-l] Fwd: problem with bioperl (where's the Mus?)
Anand C. Patel
acpatel at gmail.com
Sat Aug 22 18:44:20 EDT 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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