added to tidy things up

misc-scripts/surgery/SeqStoreConverter/vega/VBasicConverter.pm

+use strict;
+use warnings;
+
+use SeqStoreConverter::BasicConverter;
+
+package SeqStoreConverter::vega::VBasicConverter;
+
+use vars qw(@ISA);
+
+@ISA = qw(SeqStoreConverter::BasicConverter);
+
+
+sub remove_supercontigs {
+    my $self = shift;
+    
+    my $target = $self->target();
+    my $dbh    = $self->dbh();
+    $self->debug("Vega specific - removing supercontigs from $target");
+
+    $dbh->do("DELETE FROM $target.meta ". 
+	     "WHERE meta_value like '%supercontig%'");
+
+    $dbh->do("DELETE FROM $target.coord_system ".
+	     "WHERE name like 'supercontig'");
+    
+    $dbh->do("DELETE $target.a ".
+	     "FROM $target.assembly a, $target.seq_region sr ". 
+	     "WHERE sr.coord_system_id = 2 ".
+	     "and a.asm_seq_region_id = sr.seq_region_id");
+
+    $dbh->do("DELETE FROM $target.seq_region ".
+	     "WHERE coord_system_id = 2");
+}
+
+
+
+
+sub copy_other_tables {
+  my $self = shift;
+  #xref tables
+  $self->copy_tables("xref",
+                     "go_xref",
+                     "identity_xref",
+                     "object_xref",
+                     "external_db",
+                     "external_synonym",
+  #marker/qtl related tables
+                     "map",
+                     "marker",
+                     "marker_synonym",
+                     "qtl",
+                     "qtl_synonym",
+  #misc other tables
+					 "supporting_feature",
+					 "analysis",
+					 "exon_transcript",
+					 "interpro",
+					 "gene_description",
+					 "protein_feature",
+  #vega tables
+					 "gene_synonym",
+					 "transcript_info",
+					 "current_gene_info",
+					 "current_transcript_info",
+					 "author",
+					 "gene_name",
+					 "transcript_class",
+					 "gene_remark",
+					 "gene_info",
+					 "evidence",
+					 "transcript_remark",
+					 "clone_remark",
+					 "clone_info",
+					 "clone_info_keyword",
+					 "clone_lock");
+$self->copy_current_clone_info;
+}
+
+sub copy_current_clone_info {
+    my $self=shift;
+    my $source = $self->source();
+    my $target = $self->target();
+    my $sth = $self->dbh()->prepare
+        ("INSERT INTO $target.current_clone_info(clone_id,clone_info_id) SELECT * FROM $source.current_clone_info");
+    $sth->execute();
+    $sth->finish();    
+}
+
+
+
+sub update_clone_info {
+  my $self = shift;
+  return;
+}
+
+sub copy_internal_clone_names {
+	my $self = shift;
+    return;
+}