Merge 3801044 into 5d5fe27

lib/Bio/EnsEMBL/DataCheck/Checks/MTCodonTable.pm

@@ -0,0 +1,85 @@
+=head1 LICENSE
+
+Copyright [2018-2019] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the 'License');
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an 'AS IS' BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::MTCodonTable;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'MTCodonTable',
+  DESCRIPTION    => 'MT seq region has codon table attribute',
+  GROUPS         => ['core'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['core', 'otherfeatures'],
+  TABLES         => ['attrib_type', 'coord_system', 'seq_region', 'seq_region_attrib']
+};
+
+sub skip_tests {
+  my ($self) = @_;
+
+  my $sa = $self->dba->get_adaptor('Slice');
+
+  # There's no good way to detect a mitochondrial sequence,
+  # have to rely on a set of likely names.
+  my @mts = ('MT', 'Mito', 'mitochondrion_genome');
+
+  my $has_mt = 0;
+  foreach my $mt ( @mts ) {
+    my $slice = $sa->fetch_by_region('toplevel', $mt);
+    if (defined $slice) {
+      $has_mt = 1;
+      last;
+    }
+  }
+
+  if (!$has_mt) {
+    return (1, 'No mitochondrional seq_region.');
+  }
+}
+
+sub tests {
+  my ($self) = @_;
+
+  my $desc = 'MT region has codon table attribute';
+  my @mts  = ('MT', 'Mito', 'mitochondrion_genome');
+
+  my $sa = $self->dba->get_adaptor('Slice');
+
+  my $has_attribute = 0;
+  foreach my $mt ( @mts ) {
+    my $slice = $sa->fetch_by_region('toplevel', $mt);
+    if (defined $slice) {
+      my $attribs = $slice->get_all_Attributes('codon_table');
+
+      if (scalar @$attribs) {
+        $has_attribute = 1;
+        last;
+      }
+    }
+  }
+
+  ok($has_attribute, $desc);
+}
+
+1;

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -618,6 +618,15 @@
       "name" : "LRG",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::LRG"
    },
+   "MTCodonTable" : {
+      "datacheck_type" : "critical",
+      "description" : "MT seq region has codon table attribute",
+      "groups" : [
+         "core"
+      ],
+      "name" : "MTCodonTable",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::MTCodonTable"
+   },
    "MetaCoord" : {
       "datacheck_type" : "critical",
       "description" : "The meta_coord table is correctly populated",