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.
Could be done with diff alphabet


On Tue, Aug 12, 2014 at 5:28 PM, Daniel T. McDonald <
Daniel.Mcdonald@colorado.edu> wrote:

> 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>.
>>
>
>