Hmm... fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype ? That looks like a weird copy / paste error. I'd read that as at least 3 tokens: fetch_all_by_Method, LinkSpecies, and Set_orthology_type_subtype. Or then, that could also be fetch_all_by_, MethodLinkSpeciesSet (since you have that token a few lines earlier), and _orthology_type_subtype

I'd say to the author of that script: concatenatingmethodnames doesn't create new ones.

Of course I could be mistaken all together, and there's only a typo somewhere. But not having the Bio::EnsEMBL::Compara::DBSQL::MethodLinkSpeciesSetAdaptor package handy (looks like a constructed namespace, anyways), I can't tell.