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

New pull request based on latest version of QIIME codebase.
Thanks! I agree that we need a better description of this file format and how we handle taxonomy strings in general. [Here's](http://qiime.org/documentation/file_formats.html#id-to-taxonomy-map) the current documentation on the file format, feel free to add to this (not sure of a better place, @gregcaporaso can you weigh in if there is a better place to document this)?