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

New pull request based on latest version of QIIME codebase.
This would be safer to have in a try/finally, in case an error is raised during taxonomy assignment. e.g.:

```python
try:
    result = mothur.mothur_classify_file(
    ...
    )
finally:
    mothur_tax_file.close()
```