<div dir="ltr"><div>Dear Developers</div><div><br></div><div>when using the code:</div><div><br></div><div><div>#!/usr/bin/perl -w</div><div><br></div><div>use strict;</div><div>use warnings;</div><div>use Bio::EnsEMBL::Registry;</div><div><br></div><div>use_ensembl_api_version(38);</div><div><br></div><div>my $registry = 'Bio::EnsEMBL::Registry';</div><div>$registry->load_registry_from_db(---);</div><div><br></div><div>my $external_gene_adaptor       = $registry->get_adaptor("human", "otherfeatures", "gene");</div><div>my $external_transcript_adaptor = $registry->get_adaptor('human', 'otherfeatures', 'transcript');</div><div><br></div><div>foreach my $external_gene (@{$external_gene_adaptor->fetch_all_by_external_name("ASXL1") }) {</div><div><span class="" style="white-space:pre">     </span>my $refseq_transcripts =  $external_gene->get_all_Transcripts();</div><div>}</div></div><div><br></div><div><br></div><div>in API v78 , the script does what I expect and retrieves the transcripts, however , I am getting lots of errors on the transcript adapters. </div><div><br></div><div>"Use of uninitialized value $xref_display_label in substitution (s///) at /ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 1861."<br></div><div><br></div><div><br></div><div>This does not seem to happen on v75</div><div><br></div><div><br></div><div>here is error on the debugger:</div><div><br></div><div><div>Use of uninitialized value $xref_display_label in substitution (s///) at /ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 1861.</div><div> at /ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 1861.</div><div>        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</div><div>        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</div><div>        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</div><div>        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</div><div>        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</div><div>        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</div><div>        Bio::EnsEMBL::Gene::get_all_Transcripts(Bio::EnsEMBL::Gene=HASH(0x46e0718)) called at <a href="http://test_query2.pl">test_query2.pl</a> line 17</div><div>Use of uninitialized value $xref_display_label in substitution (s///) at /ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 1861.</div></div><div><br></div><div><br></div><div><br></div><div>Can you tell me if this is some bug on the lastest version?</div><div><br></div><div>Best regards</div><div><br></div><div>Duarte</div>
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