[Biopython-dev] GSoC python variant update 3

Lenna Peterson arklenna at gmail.com
Wed May 23 21:56:03 UTC 2012

Hi all,

Latest blog post here: http://arklenna.tumblr.com/post/23630012065/week-1

Brief summary:

I have reversed my prior conclusion that `SeqRecord` is inadequate for
holding variant data. It is still not ideal, but the advantages of
using an existing native object are substantial, and the disadvantages
can be reduced by creating an accessor for the variant-specific data
within a `SeqRecord`.

I've made an outline of how I would store the information returned by
PyVCF within `SeqRecord` and `SeqFeature` objects. It includes a few
questions about the most logical way to store certain variant

As the coding period has now started, I'll be pushing some prototypes
to GitHub in the near future.


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