[GSoC] GSoC python variant update 6

[Lenna Peterson]

Post: http://arklenna.tumblr.com/post/26196310200/

I've made a new branch (variant2:
https://github.com/lennax/biopython/tree/variant2 ) which has a very
skeletal outline of a set of Python objects designed to store
variants. One might note many similarities to the organization of
PyVCF. One thing SQL did neatly was store per-allele data with the
allele, rather than with the site, and I'm envisioning doing this in
Python, as well.

For a Python variant object, are there any organizational choices that
would make it easier for future conversion of a variant to HGVS
syntax? (this is primarily directed at Reece but I'm open to all
suggestions)

Another question that may reveal my complete ignorance of haplotypes
and such: could a polyploid site ever be partially phased? e.g. a
triploid genotype of 0/1|0?

Looking forward to any and all questions, comments, concerns, etc.

Lenna