[Biopython-dev] GSoC python variant update 7

[Lenna Peterson]

Hi all,

New blog post: http://arklenna.tumblr.com/post/27418058203/

Last week, Reece suggested trying to represent a variety of variants
with just five identifiers: accession, start, stop, pre_seq, and
post_seq. I've started a very minimal Variant object (in
https://github.com/lennax/biopython/blob/variant2/Bio/Variant/variant.py),
using `FeatureLocation` for its location. This uses zero-based,
right-open coordinates, similar to array counting in Python. In
contrast, HGVS and VCF both count from 1.

I've created a list of variant types each represented in HGVS, VCF (if
possible), and my new Python representation. It can be found on the
blog post. Please let me know if there are any errors in my
interpretation of these variant types.

Thanks,

Lenna