[Biopython-dev] GSoC python variant update 2

Lenna Peterson arklenna at gmail.com
Wed May 16 20:01:30 UTC 2012

Hi all, 

Latest blog post here: http://arklenna.tumblr.com/post/23178684555/week-2

Brief summary of this post: 

I don't think `SeqFeature` or an extension thereof would be appropriate for storing Variant data; therefore, I intend to make a new structure based on `_Record` and `_Call` in PyVCF. I'm not sure if this structure should be associated with `Seq`, i.e. by naming it `SeqVariant`, and would like feedback on this question. 

It could be very difficult to make PyVCF compatible with Python 2.5. Therefore, I am planning to write my project to be compatible with Python 2.6 and delaying its inclusion in the main Biopython branch until a future 2.6+ Biopython release. Alternate suggestions are welcome. 

This week I will solidify the structure so I am ready for the end of the community bonding period and the start of coding on May 21. 



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