Merge 04c0903 into 7650945

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

@@ -0,0 +1,111 @@
+=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::XrefPrefixes;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'XrefPrefixes',
+  DESCRIPTION    => 'Check that xrefs have the correct prefix for their dbprimary_acc',
+  GROUPS         => ['xref'],
+  DB_TYPES       => ['core'],
+  TABLES         => ['xref', 'external_db'],
+  PER_DB         => 1
+};
+
+sub tests {
+  my ($self) = @_;
+  my $prefixes = {
+  'BARLEX' => '^HORVU',
+  'CCDS' => '^CCDS',
+  'CL' => '^CL:',
+  'ChEBI' => '^CHEBI:',
+  'ChEMBL' => '^ChEMBL',
+  'EcoGene' => '^EG',
+  'FYPO_EXT' => '^FYPO_EXT:',
+  'FlyBaseName_gene' => '^FB',
+  'FlyBaseName_transcript' => '^FB',
+  'FlyBaseName_translation' => '^FB',
+  'GO' => '^GO:',
+  'GO_REF' => '^GO_REF:',
+  'HGNC' => '^HGNC:',
+  'Interpro' => '^IPR',
+  'MGI' => '^MGI:',
+  'MaizeGDB' => '^Zm',
+  'MetaCyc' => '^PWY-',
+  'PATO' => '^PATO:',
+  'PHI' => '^PHI:',
+  'PR' => '^PR:',
+  'PUBMED_POMBASE' => '^PMPB:',
+  'Plant_Reactome_Pathway' => '^R-',
+  'Plant_Reactome_Reaction' => '^R-',
+  'RFAM' => '^RF',
+  'RNAcentral' => '^URS',
+  'RefSeq_mRNA' => '^NM_',
+  'RefSeq_mRNA_predicted' => '^XM_',
+  'RefSeq_ncRNA' => '^NR_',
+  'RefSeq_ncRNA_predicted' => '^XR_',
+  'RefSeq_peptide' => '^^NP|^YP|^AP',
+  'RefSeq_peptide_predicted' => '^XP',
+  'SGD' => '^S',
+  'SGD_GENE' => '^S',
+  'UniParc' => '^UPI',
+  'UniPathway' => '^UPA',
+  'VGNC' => '^VGNC:',
+  'WHEATEXP_GENE' => '^Traes',
+  'WHEATEXP_TRANS' => '^Traes',
+  'Xenbase' => '^XB',
+  'ZFIND_ID' => '^ZDB',
+  'cint_aniseed_v1' => '^ci',
+  'dictyBase' => '^DDB',
+  'external_wheat_gene_names' => '^GSP-',
+  'flybase_gene_id' => '^FB',
+  'flybase_transcript_id' => '^FB',
+  'flybase_translation_id' => '^FB',
+  'goslim_goa' => '^GO:',
+  'miRBase' => '^MI',
+  'wormbase_gene' => '^WB',
+  'wormbase_gseqname' => '^WB',
+  'wormbase_locus' => '^WB'
+  };
+  while (my ($source_name, $pattern) = each(%$prefixes)) {
+    $self->xref_prefixes_check($source_name, $pattern,"All dbprimary accessions for xref $source_name are prefixed with the correct pattern: $pattern");
+  }
+}
+
+sub xref_prefixes_check {
+  my ($self,$source_name,$pattern,$desc) = @_;    
+  my $sql  = qq/
+      SELECT dbprimary_acc FROM xref x, external_db e
+      WHERE
+        x.external_db_id = e.external_db_id AND
+        e.db_name = '$source_name' AND
+        x.dbprimary_acc NOT REGEXP '$pattern'
+    /;
+  is_rows_zero($self->dba, $sql, $desc);
+}
+
+1;

lib/Bio/EnsEMBL/DataCheck/index.json

@@ -1424,6 +1424,15 @@
       "name" : "XrefHTMLBlank",
       "package_name" : "Bio::EnsEMBL::DataCheck::Checks::XrefHTMLBlank"
    },
+   "XrefPrefixes" : {
+      "datacheck_type" : "critical",
+      "description" : "Check that xrefs have the correct prefix for their dbprimary_acc",
+      "groups" : [
+         "xref"
+      ],
+      "name" : "XrefPrefixes",
+      "package_name" : "Bio::EnsEMBL::DataCheck::Checks::XrefPrefixes"
+   },
    "XrefTypes" : {
       "datacheck_type" : "advisory",
       "description" : "Xrefs are only attached to one feature type.",