[Biopython-dev] GSoC genomic variant proposal

Brad Chapman chapmanb at 50mail.com
Thu Apr 5 10:47:09 UTC 2012


> I'm linking to a revision of my GSoC proposal:
> https://docs.google.com/document/d/1txW9bwMYC6avlJxqs7x-mB-M09gxy2Uc6XqhR04y6ac/edit
> Thank you to everyone for your feedback.

This is coming along great, thanks for all the work on it. I've added a
couple of specific suggestions about iterative parsing, which PyVCF
does, and using external tools to make the coding region evaluation work

One other practical suggestion: you should add a link to the latest
version of your google doc at the top of your proposal on the GSoC
Melange site. You won't be able to edit there after Friday but can
update your google document in case of reviewer suggestions.

Thanks again and best of luck during the review process,

> Peter,
> I didn't realize Biopython has never been tested on IronPython. As I
> have no familiarity with .NET or Windows, I'll have to rescind my
> offer to test it. Sorry to get your hopes up!
> Reece,
> I've revised the prose sections and almost completely rewritten the
> timeline. This version provides more information about my background,
> a more detailed description of the overall project, and more specific
> goals.
> Brad,
> I've tried to go into as much detail as my knowledge of VCF and GVF
> structure allows. I laid out a more specific structure for both the
> backend and frontend structures for the data. I've revised the unit
> tests to be more specific and less dependent on interaction with other
> modules and I've tried to anticipate some cases that may produce
> unexpected behavior. I also highlighted specific places where the
> design should be generalizable.
> James,
> I hope my revised project description is more focused. Regarding CNV
> etc., I did not mean to specifically exclude them by mentioning SNPs,
> and I've reworded that paragraph to be more general. I get the
> impression that CNV and other structural variants are considerably
> more complex to represent and manipulate. I'd be more than happy to
> read more about breakpoint theory etc. and to prototype any specific
> workflows you might suggest.
> Lenna
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