code to get LRG from database and store in a MappedSliceContainer

modules/Bio/EnsEMBL/DBSQL/AssemblySliceAdaptor.pm

@@ -131,7 +131,7 @@ sub fetch_by_version {
   my $mapped_slice = Bio::EnsEMBL::MappedSlice->new(
       -ADAPTOR   => $self,
       -CONTAINER => $container,
-      -NAME      => $slice->name.":mapped_$version",
+      -NAME      => $slice->name."\#mapped_$version",
   );
 
   my $cs_name = $slice->coord_system_name;
@@ -162,5 +162,75 @@ sub fetch_by_version {
 }
 
 
+=head2 fetch_by_name
+
+  Arg[1]      : Bio::EnsEMBL::MappedSliceContainer $container - the container
+                  to attach MappedSlices to
+  Arg[2]      : String $name - the assembly name to fetch
+  Arg[3]      : (optional) String $version -- the version for the new assembly
+  Example     : my ($mapped_slice) = @{ $msc->fetch_by_name('LRG1','1') };
+  Description : Creates a MappedSlice representing an alternative assembly
+                version of the container's reference slice.
+  Return type : listref of Bio::EnsEMBL::MappedSlice
+  Exceptions  : thrown on wrong or missing arguments
+  Caller      : general, Bio::EnsEMBL::MappedSliceContainer
+  Status      : At Risk
+              : under development
+
+=cut
+
+sub fetch_by_name {
+  my $self = shift;
+  my $container = shift;
+  my $name = shift;
+  my $version = shift; 
+
+  # arguement check
+  unless ($container and ref($container) and
+          $container->isa('Bio::EnsEMBL::MappedSliceContainer')) {
+    throw("Need a MappedSliceContainer.");
+  }
+
+  unless ($name) {
+    throw("Need an assembly name.");
+  }
+
+  $version ||= '';
+  my $slice = $container->ref_slice;
+
+  # project slice onto other assembly and construct MappedSlice for result
+  my $mapped_slice = Bio::EnsEMBL::MappedSlice->new(
+      -ADAPTOR   => $self,
+      -CONTAINER => $container,
+      -NAME      => $slice->name."\#mapped_$name:$version",
+  );
+
+
+  foreach my $seg (@{ $slice->project($name, $version) }) {
+  
+    my $proj_slice = $seg->to_Slice;
+    
+    # create a Mapper to map to/from the mapped_slice artificial coord system
+    my $mapper = Bio::EnsEMBL::Mapper->new('mapped_slice', 'native_slice');  
+    
+    # tell the mapper how to map this segment
+    $mapper->add_map_coordinates(
+        'mapped_slice',
+        $seg->from_start,
+        $seg->from_end,
+        ($slice->strand * $proj_slice->strand),
+        $proj_slice->seq_region_name,
+        $proj_slice->start,
+        $proj_slice->end
+    );
+    
+    # add the Slice/Mapper pair to the MappedSlice
+    $mapped_slice->add_Slice_Mapper_pair($proj_slice, $mapper);
+  }
+
+  return [$mapped_slice];
+}
+
+
 1;