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

New pull request based on latest version of QIIME codebase.
I'm not sure if everything gets flushed to disk so that opening a new filehandle in `'U'` mode will have access to the entire file. It might be safer to pass `delete=False` to `NamedTemporaryFile`, close `mothur_tax_file` instead of `seek(0)`, and return `mothur_tax_file.name` (which is what the caller of this method needs anyways). Then the caller can delete the filepath in a `try/finally` below (I'll make note of this in another comment).