Merge pull request #539 from nuno-agostinho/fix/vcf-only-proteinfunct…

…ionpredictions Skip ProteinFunctionPredictions tests for VCF-only species
Ensembl · Mar 21, 2023 · bba58dc · bba58dc
2 parents 5a6db36 + ead3ae1
commit bba58dc
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Showing 3 changed files with 24 additions and 2 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/CompareProteinFunctionPredictions.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/CompareProteinFunctionPredictions.pm
@@ -36,6 +36,17 @@ use constant {
   TABLES         => ['attrib', 'protein_function_predictions', 'protein_function_predictions_attrib']
 };
 
+sub skip_tests {
+  my ($self) = @_;
+
+  my $mca = $self->dba->get_adaptor('MetaContainer');
+  my $vcf = $mca->list_value_by_key('variation_source.vcf')->[0] || 0;
+
+  if ($vcf) {
+    return( 1, "Protein function predictions are not expected for species whose variation source is VCF." );
+  }
+}
+
 sub tests {
   my ($self) = @_;
 

diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/ProteinFunctionPredictions.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/ProteinFunctionPredictions.pm
@@ -29,12 +29,23 @@ extends 'Bio::EnsEMBL::DataCheck::DbCheck';
 
 use constant {
   NAME        => 'ProteinFunctionPredictions',
-  DESCRIPTION => 'prediction_matrix is not NULL or empty',
+  DESCRIPTION => 'Protein function predictions are present and correct',
   GROUPS      => ['variation'],
   DB_TYPES    => ['variation'],
   TABLES      => ['protein_function_predictions']
 };
 
+sub skip_tests {
+  my ($self) = @_;
+
+  my $mca = $self->dba->get_adaptor('MetaContainer');
+  my $vcf = $mca->list_value_by_key('variation_source.vcf')->[0] || 0;
+
+  if ($vcf) {
+    return( 1, "Protein function predictions are not expected for species whose variation source is VCF." );
+  }
+}
+
 sub tests {
   my ($self) = @_;
 

diff --git a/lib/Bio/EnsEMBL/DataCheck/index.json b/lib/Bio/EnsEMBL/DataCheck/index.json
@@ -2174,7 +2174,7 @@
    },
    "ProteinFunctionPredictions" : {
       "datacheck_type" : "critical",
-      "description" : "prediction_matrix is not NULL or empty",
+      "description" : "Protein function predictions are present and correct",
       "groups" : [
          "variation"
       ],