[GSoC] [Biopython-dev] GSoC python variant update 2

[Brad Chapman]

Lenna;
Thanks for the update on your thinking. Sounds like you are right on
track.

> 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.

I'm agreed about SeqFeature. Would you consider using _Record/_Call
directly? Then you could provide functionality to convert this to/from
basic SeqFeatures if needed. An advantage of using these structures
explicitly is that you could plug in compatible APIs, like Aaron
Quinlan's CyVCF:

https://github.com/arq5x/cyvcf

I don't think we should add a new representation class unless we
explicitly need to store additional information.

> 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.

I'm agreed with this. I don't think 2.5 is an entrenched as 2.4 was so
think we could move on a deprecation path for it. It's more important to
be forward compatible with 3.x and 2.6+ should make that easier.

Thanks again for sharing all your thoughts and digging into this,
Brad