Merge pull request #533 from Ensembl/feature/dc_sequence_checksum

Feature/dc sequence checksum

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

@@ -0,0 +1,103 @@
+=head1 LICENSE
+
+Copyright [2018-2023] 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::SequenceChecksum;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'SequenceChecksum',
+  DESCRIPTION    => 'Check All checksum attribute are assigned to all genomic features',
+  GROUPS         => ['sequence_checksum'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['core'],
+  TABLES         => ['seq_region_attrib', 'transcript_attrib', 'translation_attrib', 'seq_region', 'transcript', 'translation']
+};
+
+sub tests {
+  my ($self) = @_;
+  my $species_id = $self->dba->species_id;
+
+  my %attrib_mapping = (
+    toplevel     => ['sha512t24u_toplevel', 'md5_toplevel'],
+    transcript   => ['sha512t24u_cds', 'md5_cds', 'sha512t24u_cdna', 'md5_cdna'],
+    translation  => ['sha512t24u_pep', 'md5_pep'],
+  );
+  my %attrib_sql = (
+    toplevel => qq/
+      SELECT COUNT(*) FROM seq_region 
+      INNER JOIN coord_system cs ON(cs.coord_system_id=seq_region.coord_system_id)
+      INNER JOIN seq_region_attrib sra ON (seq_region.seq_region_id=sra.seq_region_id)
+      INNER JOIN attrib_type at ON(at.attrib_type_id=sra.attrib_type_id)
+      WHERE  cs.species_id=? AND at.code=?
+    /,
+    transcript => qq/
+      SELECT COUNT(*) FROM transcript 
+      INNER JOIN seq_region sr ON transcript.seq_region_id = sr.seq_region_id
+      INNER JOIN coord_system cs ON sr.coord_system_id = cs.coord_system_id 
+    /,
+    translation => qq/
+      SELECT COUNT(*) FROM translation 
+      INNER JOIN transcript t ON translation.transcript_id = t.transcript_id 
+      INNER JOIN seq_region sr ON t.seq_region_id = sr.seq_region_id
+      INNER JOIN coord_system cs ON sr.coord_system_id = cs.coord_system_id 
+    /
+  );
+
+  my $helper = $self->dba->dbc->sql_helper;
+  my $feature_count;
+  my $attrib_sql;
+  foreach my $table (keys %attrib_mapping){
+   $attrib_sql = $attrib_sql{$table};
+   if( $table eq "toplevel"){
+     $feature_count  = $helper->execute_single_result(
+                       -SQL => $attrib_sql, 
+	               -PARAMS => [$species_id, $table]
+                     );
+   }else{
+
+     $attrib_sql = ($table eq "transcript") ? $attrib_sql{$table}." WHERE  cs.species_id=?" : $attrib_sql{$table}." WHERE  cs.species_id=? and t.biotype='protein_coding'"; 	   
+     $feature_count = $helper->execute_single_result(
+                       -SQL => $attrib_sql,
+                       -PARAMS => [$species_id]
+                     );
+     $attrib_sql = $attrib_sql{$table} . qq/  
+                      INNER JOIN ${table}_attrib ta ON ${table}.${table}_id = ta.${table}_id
+                      INNER JOIN attrib_type a ON ta.attrib_type_id = a.attrib_type_id
+                      WHERE cs.species_id=? AND a.code=? /;		     
+
+   }
+
+   foreach my $attrib_code (@{$attrib_mapping{$table}}){ 
+     my  $attrib_count  = $helper->execute_single_result(
+                           -SQL => $attrib_sql,
+                           -PARAMS   => [$species_id, $attrib_code]
+                          );
+     my $desc = "All $table assigned to attrib $attrib_code with checksum value";
+     cmp_ok( $feature_count , "==", $attrib_count, $desc );			  
+   }
+  }
+}
+
+1;
+

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -2443,6 +2443,15 @@
       "name" : "SeqRegionTopLevel",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::SeqRegionTopLevel"
    },
+   "SequenceChecksum" : {
+      "datacheck_type" : "critical",
+      "description" : "Check All checksum attribute are assigned to all genomic features",
+      "groups" : [
+         "sequence_checksum"
+      ],
+      "name" : "SequenceChecksum",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::SequenceChecksum"
+   },
    "SequenceLevel" : {
       "datacheck_type" : "critical",
       "description" : "DNA is attached, and only attached, to sequence-level seq_regions",