Stockholm format parser/writer

This is in the new parse format that @ElDeveloper created in #235 so merge his first.
#294 is the issue you are looking for.


On (Jun-10-14|11:01), Greg Caporaso wrote:
> > +    """
> > +
> > +    def setUp(self):
> > +        """Setup for stockholm tests."""
> > +        seqs = [DNA("ACC-G-GGTA", identifier="seq1"),
> > +                DNA("TCC-G-GGCA", identifier="seq2")]
> > +        self.aln = Alignment(seqs)
> > +        self.GF = OrderedDict({"ID": "TEST", "SQ": 2})
> > +        self.GS = OrderedDict({"seq1": {"AC": 111}, "seq2": {"AC": 222}})
> > +        self.GR = OrderedDict({"seq1": {"SS": "1110101111"},
> > +                               "seq2": {"SS": "0110101110"}})
> > +        self.GC = OrderedDict({"SS_cons": "(((....)))"})
> > +
> > +    def test_stockholm_from_alignment(self):
> > +        """ Make sure stockholm with all information contained is formatted
> > +        correctly """
> 
> Note that all of these test doc strings should be on a single line, but we also decided that these are not necessary (though I can't find the issue now to link to it) as long as the method name is descriptive, so it might just be easier to drop the docstrings from your tests. 
> 
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