Merge 5fb01ec into 0ee79ee

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

@@ -0,0 +1,59 @@
+=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::DuplicateTranscriptNames;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'DuplicateTranscriptNames',
+  DESCRIPTION    => 'Protein coding Transcript Names are unique',
+  GROUPS         => ['xref'],
+  DATACHECK_TYPE => 'advisory',
+  DB_TYPES       => ['core'],
+  TABLES         => ['transcript','xref','seq_region','coord_system']
+};
+
+sub tests {
+  my ($self) = @_;
+  my $species_id = $self->dba->species_id;
+  my $desc = 'Transcript Names are unique';
+  my $diag = 'Number of Transcripts, display_xref_id, dbprimary_acc';
+  my $sql  = qq/
+    SELECT COUNT(*), x.xref_id, x.dbprimary_acc FROM
+      transcript t INNER JOIN
+      xref x INNER JOIN
+      seq_region USING (seq_region_id) INNER JOIN
+      coord_system USING (coord_system_id)
+    WHERE t.display_xref_id=x.xref_id AND
+      t.biotype = 'protein_coding' AND
+      species_id = $species_id
+    GROUP BY x.xref_id
+    HAVING COUNT(*) > 1
+  /;
+  is_rows_zero($self->dba, $sql, $desc, $diag);
+}
+
+1;

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -549,6 +549,15 @@
       "name" : "DuplicateReadNames",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::DuplicateReadNames"
    },
+   "DuplicateTranscriptNames" : {
+      "datacheck_type" : "advisory",
+      "description" : "Protein coding Transcript Names are unique",
+      "groups" : [
+         "xref"
+      ],
+      "name" : "DuplicateTranscriptNames",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::DuplicateTranscriptNames"
+   },
    "DuplicateXref" : {
       "datacheck_type" : "critical",
       "description" : "Xrefs have been added twice with different descriptions or versions",