Immunogenicity ligandome

Instead of trying to model the space of immunogenic epitope strings directly, instead let's model immunogenicity by only keeping track of which patterns *can't* be recognized by T-cells. These are epitopes which overlap with the set of "self" peptides used for negative selection in the thymus. 
Wouldn't the os.path functions automatically handle this? e.g. path.exists("rna") == path.exists("rna/")? I assume there's something that they're not handling, but I'm curious what that is.