Merge 5f47a32 into 6e86cf4

Ensembl · Jan 23, 2020 · 61c33f7 · 61c33f7
2 parents 6e86cf4 + 5f47a32
commit 61c33f7
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Showing 4 changed files with 204 additions and 203 deletions.
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/AttribValues.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/AttribValues.pm
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/AttribValuesCoverage.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/AttribValuesCoverage.pm
@@ -0,0 +1,105 @@
+=head1 LICENSE
+
+Copyright [2018-2020] 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::AttribValuesCoverage;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'AttribValuesCoverage',
+  DESCRIPTION    => 'TSL and APPRIS covers 95% of protein-coding gene on each chromosome',
+  GROUPS         => ['geneset_support_level'],
+  DATACHECK_TYPE => 'advisory',
+  DB_TYPES       => ['core'],
+  TABLES         => ['assembly_exception', 'attrib_type', 'gene', 'seq_region', 'seq_region_attrib', 'transcript', 'transcript_attrib']
+};
+
+sub tests {
+  my ($self) = @_;
+  my $helper = $self->dba->dbc->sql_helper;
+
+  my $desc_1 = '95% of the protein-coding genes on each chromosome have APPRIS attributes';
+  my $sql_1a = q/
+    SELECT sr.name, COUNT(DISTINCT g.stable_id) FROM
+      gene g INNER JOIN
+      seq_region sr USING (seq_region_id) INNER JOIN
+      seq_region_attrib sra USING (seq_region_id) INNER JOIN
+      attrib_type at ON sra.attrib_type_id = at.attrib_type_id INNER JOIN
+      transcript t USING (gene_id) INNER JOIN
+      transcript_attrib ta USING (transcript_id) INNER JOIN
+      attrib_type at2 ON ta.attrib_type_id = at2.attrib_type_id
+    WHERE
+      g.biotype = 'protein_coding' AND
+      at.code = 'karyotype_rank' AND
+      at2.code like 'appris%'
+    GROUP BY sr.name
+  /;
+  my $sql_1b = q/
+    SELECT sr.name, COUNT(DISTINCT g.stable_id) FROM
+      gene g INNER JOIN
+      seq_region sr USING (seq_region_id) INNER JOIN
+      seq_region_attrib sra USING (seq_region_id) INNER JOIN
+      attrib_type at ON sra.attrib_type_id = at.attrib_type_id
+    WHERE
+      g.biotype = 'protein_coding' AND
+      at.code = 'karyotype_rank'
+    GROUP BY sr.name
+  /;
+  row_subtotals($self->dba, undef, $sql_1a, $sql_1b, 0.95, $desc_1);
+
+  if ($self->species =~ /(homo_sapiens|mus_musculus)/) {
+
+    my $desc_2 = '95% of the protein-coding genes on each chromosome have TSL attributes';
+    my $sql_2a = q/
+      SELECT sr.name, COUNT(DISTINCT g.stable_id) FROM
+        gene g INNER JOIN
+        seq_region sr USING (seq_region_id) INNER JOIN
+        seq_region_attrib sra USING (seq_region_id) INNER JOIN
+        attrib_type at ON sra.attrib_type_id = at.attrib_type_id INNER JOIN
+        transcript t USING (gene_id) INNER JOIN
+        transcript_attrib ta USING (transcript_id) INNER JOIN
+        attrib_type at2 ON ta.attrib_type_id = at2.attrib_type_id
+      WHERE
+        g.biotype = 'protein_coding' AND
+        at.code = 'karyotype_rank' AND
+        at2.code like 'tsl%'
+      GROUP BY sr.name
+    /;
+    my $sql_2b = q/
+      SELECT sr.name, COUNT(DISTINCT g.stable_id) FROM
+        gene g INNER JOIN
+        seq_region sr USING (seq_region_id) INNER JOIN
+        seq_region_attrib sra USING (seq_region_id) INNER JOIN
+        attrib_type at ON sra.attrib_type_id = at.attrib_type_id
+      WHERE
+        g.biotype = 'protein_coding' AND
+        at.code = 'karyotype_rank'
+      GROUP BY sr.name
+    /;
+    row_subtotals($self->dba, undef, $sql_2a, $sql_2b, 0.95, $desc_2);
+  }
+}
+
+1;
diff --git a/lib/Bio/EnsEMBL/DataCheck/Checks/AttribValuesExist.pm b/lib/Bio/EnsEMBL/DataCheck/Checks/AttribValuesExist.pm
@@ -0,0 +1,85 @@
+=head1 LICENSE
+
+Copyright [2018-2020] EMBL-European Bioinformatics Institute
+
+Licensed under the Apache License, Version 2.0 (the 'License');
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an 'AS IS' BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+
+=cut
+
+package Bio::EnsEMBL::DataCheck::Checks::AttribValuesExist;
+
+use warnings;
+use strict;
+
+use Moose;
+use Test::More;
+use Bio::EnsEMBL::DataCheck::Test::DataCheck;
+
+extends 'Bio::EnsEMBL::DataCheck::DbCheck';
+
+use constant {
+  NAME           => 'AttribValuesExist',
+  DESCRIPTION    => 'Check that TSL, APPRIS and GENCODE attributes exist',
+  GROUPS         => ['geneset_support_level'],
+  DATACHECK_TYPE => 'critical',
+  DB_TYPES       => ['core'],
+  TABLES         => ['attrib_type', 'transcript', 'transcript_attrib']
+};
+
+sub tests {
+  my ($self) = @_;
+  my $helper = $self->dba->dbc->sql_helper;
+
+  my $desc_1 = 'APPRIS attributes exist';
+  my $sql_1  = q/
+    SELECT COUNT(*) FROM
+      transcript INNER JOIN
+      transcript_attrib USING (transcript_id) INNER JOIN
+      attrib_type USING (attrib_type_id)
+    WHERE code like 'appris%'
+  /;
+  is_rows_nonzero($self->dba, $sql_1, $desc_1);
+
+  if ($self->species =~ /(homo_sapiens|mus_musculus)/) {
+    my $desc_2 = 'All genes have at least one transcript with a gencode_basic attribute';
+    my $sql_2a = q/
+      SELECT COUNT(distinct gene_id) FROM transcript
+      WHERE biotype NOT IN ('LRG_gene')
+    /;
+    my $sql_2b = q/
+      SELECT COUNT(distinct gene_id) FROM
+        transcript INNER JOIN
+        transcript_attrib USING (transcript_id) INNER JOIN
+        attrib_type USING (attrib_type_id) 
+      WHERE
+        biotype NOT IN ('LRG_gene') AND
+        attrib_type.code = 'gencode_basic'
+    /;
+
+    my $gene_count    = $helper->execute_single_result( -SQL => $sql_2a );
+    my $gencode_count = $helper->execute_single_result( -SQL => $sql_2b );
+    is($gencode_count, $gene_count, $desc_2);
+
+    my $desc_3 = 'TSL attributes exist';
+    my $sql_3  = q/
+      SELECT COUNT(*) FROM
+        transcript INNER JOIN
+        transcript_attrib USING (transcript_id) INNER JOIN
+        attrib_type USING (attrib_type_id)
+      WHERE code like 'tsl%'
+    /;
+    is_rows_nonzero($self->dba, $sql_3, $desc_3);
+  }
+}
+
+1;