Updated to reflect the fact that gene descriptions are now held in the gene...

Updated to reflect the fact that gene descriptions are now held in the gene table not in a separate gene_description table.

misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm

@@ -1824,7 +1824,7 @@ sub do_upload {
 
   # TODO warn if table not empty
 
-  foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "gene_description", "go_xref", "interpro") {
+  foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "go_xref", "interpro") {
 
     my $file = $ensembl->dir() . "/" . $table . ".txt";
 
@@ -1853,6 +1853,12 @@ sub do_upload {
     #close(DX_TXT);
   }
 
+  # gene descriptions
+  my $file = $ensembl->dir() . "/gene_description.sql";
+  print "Setting gene descriptions from $file\n";
+  my $str = "mysql -u " .$core_db->username() ." -p" . $core_db->password() . " -h " . $core_db->host() ." -P " . $core_db->port() . " " .$core_db->dbname() . " < $file";
+  system $str;
+
 }
 
 # Delete (or set some fields to null) existing data
@@ -1865,9 +1871,7 @@ sub delete_existing {
   my $core_db = $ensembl->dbc;
   # xref.txt etc
 
-  # TODO warn if table not empty
-
-  foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "gene_description", "go_xref", "interpro") {
+  foreach my $table ("xref", "object_xref", "identity_xref", "external_synonym", "go_xref", "interpro") {
 
     my $sth = $core_db->prepare("DELETE FROM $table");
     print "Deleting existing data in $table\n";
@@ -1884,6 +1888,11 @@ sub delete_existing {
 
   }
 
+  # gene descriptions
+  my $sth = $core_db->prepare("UPDATE gene SET description=NULL");
+  print "Setting all existing descriptions in gene table to null\n";
+  $sth->execute();
+
 }
 
 # Assign gene descriptions
@@ -1945,7 +1954,7 @@ sub build_gene_descriptions {
   print "Regexp filtering (" . scalar(@regexps) . " regexps) removed $removed descriptions, left with " . scalar(keys %xref_descriptions) . "\n";
 
   my $dir = $self->core->dir();
-  open(GENE_DESCRIPTIONS,">$dir/gene_description.txt") || die "Could not open $dir/gene_description.txt";
+  open(GENE_DESCRIPTIONS,">$dir/gene_description.sql") || die "Could not open $dir/gene_description.sql";
 
   # Foreach gene, get any xrefs associated with its transcripts or translations
 
@@ -1998,7 +2007,8 @@ sub build_gene_descriptions {
       my $source = $xref_to_source{$best_xref};
       my $acc = $xref_accessions{$best_xref};
 
-      print GENE_DESCRIPTIONS "$gene_id\t$description" . " [Source:$source;Acc:$acc]\n" if ($description);
+      my $desc = $description . " [Source:$source;Acc:$acc]";
+      print GENE_DESCRIPTIONS "UPDATE gene SET description='$desc' WHERE gene_id=$gene_id\n" if ($description);
 
     }