Fixes #1025, spaces in id-to-taxonomy file break assignment with Mothur.

New pull request based on latest version of QIIME codebase.
I think we can run into duplicate mappings even with the underscore escaping. For example, `a<space><space>b` and `a_b` would both map to `a__b`. Can you raise an error if `mothur_taxon` is already in `self._original_taxa` (unless there's a better way to handle this)?