Merge pull request #501 from Ensembl/update/gene_biotypes_fix

fixes for GeneBiotypes DC
Ensembl · Sep 14, 2022 · 6be0118 · 6be0118
2 parents facfc83 + 6058003
commit 6be0118
Showing 1 changed file with 23 additions and 18 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/GeneBiotypes.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/GeneBiotypes.pm
@@ -139,27 +139,32 @@ sub biotype_groups {
   my $mca = $self->dba->get_adaptor('MetaContainer');
   if($mca->single_value_by_key('genebuild.method') eq 'projection_build'){
       if (scalar(@group_mismatch) > 100){
-	  my $desc_proj = 'found no more that 100 genes with mismatched transcript biotype groups';
-	  is(scalar(@group_mismatch), 100, $desc_proj);
+	  my $desc_proj_1 = 'found no more that 100 genes with mismatched transcript biotype groups';
+	  is(scalar(@group_mismatch), 100, $desc_proj_1);
       }
-  
-      else {
-        my $desc_1 = 'genes have at least one transcript with a matching biotype group';
-        is(scalar(@group_mismatch), 0, $desc_1);
+
+     if (scalar(@pseudogene_mismatch) > 5){
+        my $desc_proj_2 = 'found no more that 5 pseudogenes that have coding transcripts';
+        is(scalar(@polymorphic_mismatch), 5, $desc_proj_2);
       }
+
      if (scalar(@polymorphic_mismatch) > 5){
-        my $desc_proj = 'found no more that 5 polymorphic_pseudogene with mismatched transcript biotype groups';
-        is(scalar(@polymorphic_mismatch), 5, $desc_proj);
-         }
-
-     else{
-        my $desc_3 = '"polymorphic_pseudogene" genes have at least one polymorphic_pseudogene transcript';
-        is(scalar(@polymorphic_mismatch), 0, $desc_3);
-     }
-     }
-
-  my $desc_2 = '"pseudogene" genes do not have coding transcripts';
-  is(scalar(@pseudogene_mismatch), 0, $desc_2);
+        my $desc_proj_3 = 'found no more that 5 polymorphic_pseudogene with mismatched transcript biotype groups';
+        is(scalar(@polymorphic_mismatch), 5, $desc_proj_3);
+      }
+  }
+  else{
+
+      my $desc_1 = 'genes have at least one transcript with a matching biotype group';
+      is(scalar(@group_mismatch), 0, $desc_1);
+
+      my $desc_2 = '"pseudogene" genes do not have coding transcripts';
+      is(scalar(@pseudogene_mismatch), 0, $desc_2);
+
+      my $desc_3 = '"polymorphic_pseudogene" genes have at least one polymorphic_pseudogene transcript';
+      is(scalar(@polymorphic_mismatch), 0, $desc_3);
+  }
+
 
 }
 1;