Merge pull request #331 from aparton/feature/filterchange95

Updated xref dumping code
Ensembl · Nov 27, 2018 · cb09ac7 · cb09ac7
2 parents 2f676c0 + e570f5c
commit cb09ac7
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Transcript.pm b/modules/Bio/EnsEMBL/VEP/AnnotationSource/Database/Transcript.pm
@@ -542,7 +542,7 @@ sub prefetch_gene_ids {
     {
       my $xref_obj = $tr->{_gene}->display_xref;
       $tr->get_Gene()->stable_id($entries[0]->{primary_id});
-      $tr->{_gene_symbol}  = $xref_obj ? $xref_obj->display_id : $entries[0]->{primary_id};
+      $tr->{_gene_symbol}  = $xref_obj ? $xref_obj->display_id : $entries[0]->{display_id};
       $tr->{_gene_symbol_source} = $entries[0]->{dbname};
       $tr->{_gene_symbol_id} = $entries[0]->{primary_id};
       $tr->{_gene_hgnc_id} = $entries[0]->{primary_id} if $entries[0]->{dbname} eq 'HGNC';

diff --git a/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm b/modules/Bio/EnsEMBL/VEP/AnnotationType/Transcript.pm
@@ -211,14 +211,18 @@ sub filter_transcript {
       # or 4540 for MT transcripts
       (
         $self->{source_type} eq 'refseq' &&
-        ($t->stable_id || '') !~ /^[A-Z]{2}\_\d+|^\d{4}$/
-      ) ||
+        !(($t->stable_id || '') =~ /^[A-Z]{2}\_\d+|^\d{4}$/ || 
+        (defined($t->display_xref) && ($t->display_xref->{display_id} || '') =~ /^[A-Z]{2}\_\d+|^\d{4}$/))
+      ) 
+
+      ||
 
       # and the same from the merged cache
       (
         $self->{source_type} eq 'merged' &&
         ($t->{_source_cache} || '') eq 'RefSeq' &&
-        ($t->stable_id || '') !~ /^[A-Z]{2}\_\d+|^\d{4}$/
+        !(($t->stable_id || '') =~ /^[A-Z]{2}\_\d+|^\d{4}$/ || 
+        (defined($t->display_xref) && ($t->display_xref->{display_id} || '') =~ /^[A-Z]{2}\_\d+|^\d{4}$/))
       )
     )
   ) {