Merge branch 'postreleasefix/100' into release/100

Ensembl · Mar 17, 2020 · 337a564 · 337a564
2 parents 3c13a87 + 8a83c60
commit 337a564
Showing 1 changed file with 6 additions and 1 deletion.
diff --git a/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Transcript.pm b/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Transcript.pm
@@ -250,7 +250,12 @@ sub get_features_by_regions_uncached {
         # skip those from analysis refseq_human_import and refseq_mouse_import
         next if $self->{core_type} eq 'otherfeatures' && $self->assembly !~ /GRCh37/i && $tr->analysis && $tr->analysis->logic_name =~ /^refseq_[a-z]+_import$/;
 
-        if($self->{core_type} eq 'otherfeatures' && defined($tr->display_xref)){
+	## Due to the inclusion of the new RefSeq transcript set (mapped from 38) into the 37 otherfeatures database,
+	## older, lower quality transcripts have been removed from the cache files. To do this, we filter out all transcripts
+	## with the analysis logic_name 'refseq_import' or 'refseq_human_import'. 
+	## All new transcripts have the logic name 'refseq_import_grch38'
+	next if $self->{core_type} eq 'otherfeatures' && $self->assembly =~ /GRCh37/i && $tr->analysis && $tr->analysis->logic_name =~ /^refseq.+import$/;
+	if($self->{core_type} eq 'otherfeatures' && defined($tr->display_xref)){
 	         $tr->{stable_id} = $tr->display_xref->{display_id};
         }