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

New pull request based on latest version of QIIME codebase.
The buffer is flushed when `seek(0)` is called ([Python docs](https://docs.python.org/2/library/io.html#io.BufferedWriter)).  I think the seek method is customary when writing to temp files for reading later on.  Happy to change to suit QIIME conventions, though.

I'll let NamedTemporaryFile manage the cleanup, but call `mothur_tax_file.close()` after the app runs.