ENH: Add iter_regex and find_features

Fixes #612. Adds iter_regex to skbio._sequence.BiologicalSequence and
find_features to skbio._sequence.NucleotideSequence. Supported features are
currently purine_run and pyrimidine run, but more can be added by specifying
additional regular expressions.
Simplify the regex considerably

Not quite sure what I was thinking with that one
Add option to allow gaps
Move feature types into class hierarchy

Also add some additional tests
Merge branch 'master' of https://github.com/biocore/scikit-bio into issue-612

Conflicts:
	skbio/sequence/tests/test_sequence.py
Adding clustal output
Adding clustal output
Correcting doctests
Registering reader/writer
Adding in test_clustal.py file
Conforming to decorator format
Modifying documentation
Correcting import module
Removing assertEqualsItems
Removing redundant documentation
Removing old clustal parser`
Merge remote-tracking branch 'upstream/master'
Merge remote-tracking branch 'upstream/master'

Conflicts:
	skbio/io/__init__.py
Correcting toctree
More corrections to toctree