[ensembl-dev] error warnings with external_adaptor fetch_by_stable_id

[Duarte Molha]

Dear Developers

when using the code:

#!/usr/bin/perl -w

use strict;
use warnings;
use Bio::EnsEMBL::Registry;

use_ensembl_api_version(38);

my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_registry_from_db(---);

my $external_gene_adaptor       = $registry->get_adaptor("human",
"otherfeatures", "gene");
my $external_transcript_adaptor = $registry->get_adaptor('human',
'otherfeatures', 'transcript');

foreach my $external_gene
(@{$external_gene_adaptor->fetch_all_by_external_name("ASXL1") }) {
my $refseq_transcripts =  $external_gene->get_all_Transcripts();
}


in API v78 , the script does what I expect and retrieves the transcripts,
however , I am getting lots of errors on the transcript adapters.

"Use of uninitialized value $xref_display_label in substitution (s///) at
/ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 1861."


This does not seem to happen on v75


here is error on the debugger:

Use of uninitialized value $xref_display_label in substitution (s///) at
/ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 1861.
 at /ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 1861.

Bio::EnsEMBL::DBSQL::TranscriptAdaptor::_objs_from_sth(Bio::EnsEMBL::DBSQL::TranscriptAdaptor=HASH(0x400deb0),
Bio::EnsEMBL::DBSQL::StatementHandle=HASH(0x4a6af68), undef,
Bio::EnsEMBL::Slice=HASH(0x46e07d8)) called at
/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line 487

Bio::EnsEMBL::DBSQL::BaseAdaptor::generic_fetch(Bio::EnsEMBL::DBSQL::TranscriptAdaptor=HASH(0x400deb0),
"t.gene_id = 127710 AND t.seq_region_id IN (131538) AND t.seq_"..., undef,
Bio::EnsEMBL::Slice=HASH(0x46e07d8)) called at
/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm line 895

Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_get_by_Slice(Bio::EnsEMBL::DBSQL::TranscriptAdaptor=HASH(0x400deb0),
Bio::EnsEMBL::Slice=HASH(0x46e07d8), "t.gene_id = 127710") called at
/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm line 911

Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::_slice_fetch(Bio::EnsEMBL::DBSQL::TranscriptAdaptor=HASH(0x400deb0),
Bio::EnsEMBL::Slice=HASH(0x46e07d8), "t.gene_id = 127710") called at
/ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm line 481

Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::fetch_all_by_Slice_constraint(Bio::EnsEMBL::DBSQL::TranscriptAdaptor=HASH(0x400deb0),
Bio::EnsEMBL::Slice=HASH(0x46e07d8), "t.gene_id = 127710") called at
/ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 338

Bio::EnsEMBL::DBSQL::TranscriptAdaptor::fetch_all_by_Gene(Bio::EnsEMBL::DBSQL::TranscriptAdaptor=HASH(0x400deb0),
Bio::EnsEMBL::Gene=HASH(0x46e0718)) called at
/ensembl/modules/Bio/EnsEMBL/Gene.pm line 998

Bio::EnsEMBL::Gene::get_all_Transcripts(Bio::EnsEMBL::Gene=HASH(0x46e0718))
called at test_query2.pl line 17
Use of uninitialized value $xref_display_label in substitution (s///) at
/ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 1861.



Can you tell me if this is some bug on the lastest version?

Best regards

Duarte
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150311/c82b1715/attachment.html>