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.
https://github.com/biocore/scikit-bio/issues/611


On Tue, Aug 12, 2014 at 5:26 PM, adamrp <notifications@github.com> wrote:

> In skbio/sequence/_sequence.py:
>
> > @@ -1324,6 +1350,34 @@ def reverse_complement(self):
> >          return self._complement(reversed(self))
> >      rc = reverse_complement
> >
> > +    def find_features(self, feature_type, min_length=1):
> > +        """Search the sequence for features
> > +
> > +        Parameters
> > +        ----------
> > +        feature_type : {'purine_run', 'pyrimidine_run'}
>
> Oh, I missed that discussion, sorry, can you link me to it? I didn't see
> it in #612 <https://github.com/biocore/scikit-bio/issues/612> or the original
> stack overflow post
> <http://stackoverflow.com/questions/25211905/determine-length-of-polypurine-tract>
> that led to the creation of that issue. What would a
> PurinePyrimidineSequence be? Isn't a nucleotide sequence just a sequence
> of purines and pyrimidines?
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/biocore/scikit-bio/pull/613/files#r16149825>.
>