[ensembl-dev] Enumerating repeat types for get_all_RepeatFeatures()

[John Marshall]

I recently noticed from the documentation that Bio::EnsEMBL::Slice::get_all_RepeatFeatures() can optionally take a repeat type argument to limit the types of repeat feature returned:

	Example: @repeat_feats = @{$slice->get_all_RepeatFeatures(undef,'LTR')};

This is very convenient for one of my scripts, which, for any requested species, dumps out a selection of repeat features arranged by type.  However there doesn't appear to be a way to enumerate all the extant repeat types for a given species -- while the type names appear to be fairly standardised, some species are missing a few of them and I wouldn't want to assume that I had seen all possibilities.

I solved this in my script with the following hackish function:

# Returns the set of all types of repeat features in $adaptor's species.
sub fetch_all_repeat_types {
  my ($adaptor) = @_;

  my ($sth, @types, $repeat_type);
  $sth = $adaptor->prepare("SELECT DISTINCT repeat_type FROM repeat_consensus");
  $sth->execute();
  $sth->bind_columns(\$repeat_type);
  while ($sth->fetch()) { push @types, $repeat_type }
  return @types;
}

but of course this makes the script susceptible to schema changes, and ideally such a function would instead be available as Bio::EnsEMBL::DBSQL::RepeatConsensusAdaptor::fetch_all_repeat_types() or similar.  (Admittedly this is probably opening a can of worms as there may well be many other items that could use similar enumeration functions...)

Any thoughts as to the right way to do this?

Thanks,

    John