[Biopython] gff3 problem

[Brad Chapman]

Leighton and Peter;

> > Just to further complicate matters, the symbol convention for GFF3 differs
> > from Biopython in terms of the categories it defines:
> > + is positive strand
> > - is negative strand
> > . is not stranded (i.e. strand not relevant)
> > ? is strand relevant, but not known
> > http://www.sequenceontology.org/gff3.shtml

Yes, although this strikes me a bit like fuzzy features in terms of
usefulness. 

> > The latter two are distinct, but not distinguished by convention in
> > Biopython:
> > The obvious (to me) mapping of the four allowed Biopython symbols to the
> > GFF3 convention is:
> > +1 -> +
> > -1 -> -
> > None -> .
> > 0 -> ?
> > because 'None' is semantically close to 'has no strand information of
> > consequence', and 0 is the mean of +1 and -1 ;)

That's fine by me. Right now both '?' and '.' are converted to None
so I lose the subtle distinction GFF is introducing:

strand_map = {'+' : 1, '-' : -1, '?' : None, None: None}

If everyone agrees on that coding it's no problem to swap it over.
Brad