Added XrefMapper module specific for S. cerevisiae mapping

misc-scripts/xref_mapping/XrefMapper/saccharomyces_cerevisiae.pm

+package XrefMapper::saccharomyces_cerevisiae;
+
+use  XrefMapper::BasicMapper;
+
+use vars qw(@ISA);
+
+@ISA = qw(XrefMapper::BasicMapper);
+
+
+sub get_set_lists {
+
+  return [["ExonerateGappedBest1", ["saccharomyces_cerevisiae","*"]]];
+
+}
+
+
+
+# Cerevisiae is imported from SGD. The gene and transcript stable IDs
+# are the SGD identifiers. The display_xref_ids for genes and
+# transcripts are calculated directly rather than via the more complex
+# priority-based method in BasicMapper.pm
+
+sub build_display_xrefs {
+
+  my ($self, $type, $external_db) = @_;
+
+  print "Setting $type display_xrefs from $type stable IDs\n";
+  my $dir = $self->core()->dir();
+
+  my $sql = "UPDATE $type t, ${type}_stable_id s, xref x, external_db e SET t.display_xref_id=x.xref_id WHERE t.${type}_id=s.${type}_id AND s.stable_id=x.dbprimary_acc AND e.external_db_id=x.external_db_id AND e.db_name=\'${external_db}\'\n";
+
+  open (SQL, ">$dir/${type}_display_xref.sql");
+
+  print SQL $sql;
+
+  close(SQL);
+
+}
+
+
+sub transcript_display_xref_sources {
+    my $self     = shift;
+    my $fullmode = shift;
+
+    my @list = qw(
+                SGD_GENE
+                SGD_TRANSCRIPT
+               );
+    
+    my %ignore;
+    
+    
+    # Both methods
+    
+    if(!$fullmode){
+	$ignore{"EntrezGene"}= 'FROM:RefSeq_[pd][en][pa].*_predicted';
+    }
+    else{
+	$ignore{"EntrezGene"} = 'select ox.object_xref_id from object_xref ox, dependent_xref dx, source s1, xref x1, source s2, xref x2 where ox.object_xref_id = dx.object_xref_id and dx.dependent_xref_id = x1.xref_id and x1.source_id = s1.source_id and s1.name = "EntrezGene" and x2.xref_id = dx.master_xref_id and x2.source_id = s2.source_id and (s2.name like "Refseq_dna_predicted" or s2.name like "RefSeq_peptide_predicted") and ox.ox_status = "DUMP_OUT"';
+	
+    }
+    
+    return [\@list,\%ignore];
+}
+
+sub gene_description_sources {
+  return (
+          "SGD_GENE"
+         );
+}
+
+
+sub gene_description_filter_regexps {
+
+  return ();
+
+}
+
+
+
+1;