My attempted script.

project_features_generic.pl

#!/usr/bin/env perl

# Projects generic features ... hopefully

use strict;
use warnings;

use Data::Dumper;

use Bio::EnsEMBL::Registry;

my $registry_file = "./myreg.pm";
my $feature       = "VariationFeature";
my $species       = "hordeum_vulgare";
my $type          = "variation";

warn "Loading the registry\n";
Bio::EnsEMBL::Registry->load_all( $registry_file )
    or die;

warn "Getting a datbase adaptor\n";
my $db_adaptor = Bio::EnsEMBL::Registry->
    get_DBAdaptor($species, $type)
    or die;

warn "Getting a feature adaptor ($feature)\n";
my $f_adaptor = $db_adaptor->
    get_adaptor($feature)
    or die;

# warn "Counting features ($feature)\n";
# warn "There are ", $f_adaptor->generic_count, " ", $feature, "s\n";

warn "Getting a feature itterator ($feature)\n";
my $f_iterator = $f_adaptor->
    fetch_Iterator
    or die;



warn "Itterating over features ($feature)\n";
while(my $f = $f_iterator->next){
    ## debugging
    next if $f->name eq "tmp_morex_contig_4_27";
    next if $f->name eq "tmp_morex_contig_4_478";
    
    warn "Working on ", $f->name, "\n";
    
    warn
        join("\t",
             $f->coord_system_name,
             $f->seq_region_name,
             $f->start,
             $f->end,
             $f->strand,
        ), "\n";
        
    warn "Projecting to toplevel\n";
    my $fp = $f->transform('toplevel')
        or die;
    
    warn
        join("\t",
             $fp->coord_system_name,
             $fp->seq_region_name,
             $fp->start,
             $fp->end,
             $fp->strand,
        ), "\n";
    
    ## Store the new slice in the old feature
    
    ## This fails
    # $f->slice( $fp->slice )
    #     or die;

    $f->start  ( $fp->start  );
    $f->end    ( $fp->end    );
    $f->strand ( $fp->strand );
    $f->slice  ( $fp->slice  ); # Does coord_system and seq_region.name
    
    $f_adaptor->update( $f )
        or die;
    
    warn
        join("\t",
             $f->coord_system_name,
             $f->seq_region_name,
             $f->start,
             $f->end,
             $fp->strand,
        ), "\n";
    
    warn "\n";
    exit;
}