Merge pull request #526 from MatBarba/mbarba/brc4

Mbarba/brc4
Ensembl · Feb 15, 2023 · ed6b16f · ed6b16f
2 parents 83e8cfd + cc5b240
commit ed6b16f
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Showing 3 changed files with 7 additions and 7 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/CompareMetaKeys.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/CompareMetaKeys.pm
@@ -30,7 +30,7 @@ extends 'Bio::EnsEMBL::DataCheck::DbCheck';
 use constant {
   NAME        => 'CompareMetaKeys',
   DESCRIPTION => 'Ensure that appropriate meta_keys are updated when the assembly or geneset changes',
-  GROUPS      => ['assembly', 'brc4_core', 'core', 'geneset', 'meta'],
+  GROUPS      => ['assembly', 'core', 'geneset', 'meta'],
   DB_TYPES    => ['core'],
   TABLES      => ['assembly', 'attrib_type', 'biotype', 'coord_system', 'exon', 'exon_transcript', 'gene', 'meta', 'seq_region', 'seq_region_attrib', 'transcript', 'translation']
 };

diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/MitochondriaAnnotated.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/MitochondriaAnnotated.pm
@@ -35,12 +35,14 @@ use constant {
   TABLES         => ['attrib_type', 'coord_system', 'seq_region', 'seq_region_attrib']
 };
 
+my @known_mt_names = ('chrMT', 'MT', 'Mito', 'mitochondrion_genome');
+
 sub skip_tests {
   my ($self) = @_;
 
   my $sa = $self->dba->get_adaptor('Slice');
 
-  my %mt_names = map { lc($_) => 1 } ('chrM', 'chrMT', 'MT', 'Mito', 'mitochondrion_genome');
+  my %mt_names = map { lc($_) => 1 } @known_mt_names;
 
   my $mt = 0;
   foreach my $mt_name (keys %mt_names) {
@@ -67,8 +69,7 @@ sub tests {
 
   my $sa = $self->dba->get_adaptor('Slice');
 
-  my @names = ('chrM', 'chrMT', 'MT', 'Mito', 'mitochondrion_genome');
-  foreach my $name (@names) {
+  foreach my $name (@known_mt_names) {
     my $slice = $sa->fetch_by_region('toplevel', $name);
     if (defined $slice) {
       my $desc_mt = "$name has mitochondrial 'sequence_location' attribute";

diff --git a/lib/Bio/EnsEMBL/DataCheck/index.json b/lib/Bio/EnsEMBL/DataCheck/index.json
@@ -798,7 +798,6 @@
       "description" : "Ensure that appropriate meta_keys are updated when the assembly or geneset changes",
       "groups" : [
          "assembly",
-         "brc4_core",
          "core",
          "geneset",
          "meta"
@@ -2719,8 +2718,8 @@
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::Variation"
    },
    "VariationAncestralAllele" : {
-	  "datacheck_type" : "advisory",
-	  "description" : "Ancestral alleles for COSMIC and ClinVar variant sources are present",
+      "datacheck_type" : "advisory",
+      "description" : "Ancestral alleles for COSMIC and ClinVar variant sources are present",
       "groups" : [
          "variation_import"
       ],