The goal of the README is to provide a minimal example of working code that gives newcomers a quick impression about what this module delivers. I don't think it is necessary to discuss subtleties of file formats here, or provide fully generic code.

Perhaps all that's needed is a small example RefSeqGenes file with Ensembl IDs and a test for reading such files.  Also another test to ensure everything works when a transcript has `version=None`.  This would also prevent regressions.

Perhaps some of these details are better to include in the docstring of `hgvs.utils.read_transcripts()`?