Add boxer to phenotypes

Ensembl · Aug 11, 2021 · f552362 · f552362
1 parent 6382397
commit f552362
Show file tree

Hide file tree

Showing 3 changed files with 13 additions and 6 deletions.
diff --git a/modules/Bio/EnsEMBL/Variation/Pipeline/PhenotypeAnnotation/CheckPhenotypeAnnotation.pm b/modules/Bio/EnsEMBL/Variation/Pipeline/PhenotypeAnnotation/CheckPhenotypeAnnotation.pm
@@ -118,7 +118,7 @@ sub write_output {
 
   #if these is a decrease in the number of entries, then stop the flow
   if (!$count_ok){
-    $self->print_logFH("ERROR: check counts failed! No futher jobs will be triggerd!\n".
+    $self->print_logFH("ERROR: check counts failed! No futher jobs will be triggered!\n".
                        "PLEASE check import and redo import if needed!");
     close($self->logFH) if defined $self->logFH ;
     close($self->pipelogFH) if defined $self->pipelogFH ;
@@ -382,7 +382,6 @@ sub check_source {
 
   # check only source specific if source specific check
   if (defined $source && defined $previous_counts->{phenotype_feature_count_details} ){
-
     my $source_name = $source->{source_name};
     $source_name = 'Animal_QTLdb_QTL' if $source_name eq 'AnimalQTLdb';
     my @check_names= grep {/$source_name/ } keys $previous_counts->{phenotype_feature_count_details};
@@ -450,4 +449,3 @@ sub update_meta{
 }
 
 1;
-
diff --git a/modules/Bio/EnsEMBL/Variation/Pipeline/PhenotypeAnnotation/Constants.pm b/modules/Bio/EnsEMBL/Variation/Pipeline/PhenotypeAnnotation/Constants.pm
@@ -116,7 +116,7 @@ use constant SPECIES => ( 'RGD'       => ['rattus_norvegicus'],
                           'ANIMALQTL' => ['bos_taurus', 'gallus_gallus', 'equus_caballus',
                                           'sus_scrofa', 'ovis_aries', 'ovis_aries_rambouillet'],
                           'OMIA'      => ['felis_catus','gallus_gallus','capra_hircus',
-                                          'bos_taurus','canis_lupus_familiaris','equus_caballus',
+                                          'bos_taurus','canis_lupus_familiaris','equus_caballus','canis_lupus_familiarisboxer',
                                           'macaca_mulatta','sus_scrofa','ovis_aries', 'ovis_aries_rambouillet',
                                           'meleagris_gallopavo', 'pan_troglodytes'],
 
@@ -137,7 +137,7 @@ use constant SPECIES => ( 'RGD'       => ['rattus_norvegicus'],
                           'ontology'  => ['homo_sapiens', 'gallus_gallus',
                                           'sus_scrofa', 'bos_taurus',
                                           'equus_caballus', 'ovis_aries', 'ovis_aries_rambouillet',
-                                          'capra_hircus', 'canis_lupus_familiaris']
-                        );
+                                          'capra_hircus', 'canis_lupus_familiaris','canis_lupus_familiarisboxer']
+    );
 
 1;
diff --git a/modules/Bio/EnsEMBL/Variation/Pipeline/PhenotypeAnnotation/ImportOMIA.pm b/modules/Bio/EnsEMBL/Variation/Pipeline/PhenotypeAnnotation/ImportOMIA.pm
@@ -283,6 +283,15 @@ sub split_omia {
       die("there was an error running as ($flat_cmd: $stderr)");
     }
   }
+
+  #dog stands for canis_lupus_familiaris and canis_lupus_familiarisboxer
+  if (-e  "$workdir/omia_split/$prefix"."canis_lupus_familiaris".$suffix) {
+    my $cmd = "cp -p $workdir/omia_split/$prefix"."canis_lupus_familiaris$suffix $workdir/omia_split/$prefix"."canis_lupus_familiarisboxer$suffix";
+    my ($return_value, $stderr, $flat_cmd) = $self->run_system_command($cmd);
+    if ($return_value) {
+      die("there was an error running as ($flat_cmd: $stderr)");
+    }
+  }
 }