[ensembl-dev] error warnings with external_adaptor fetch_by_stable_id

[Kieron Taylor]

Dear Duarte,

Those warnings are harmless, and an update of your 78 code from github should silence them. This only applies to release 78 because of a data bug.

Regards,

Kieron


Kieron Taylor PhD.
Ensembl Core senior software developer

EMBL, European Bioinformatics Institute





> On 11 Mar 2015, at 16:30, Duarte Molha <duartemolha at gmail.com> wrote:
> 
> 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
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