[Biopython-dev] GSoC python variant update

[Lenna Peterson]

Full post: http://arklenna.tumblr.com/post/28890255191/

Summary:

* I'm working on the coordinate mapper Reece contributed:
http://biopython.org/pipermail/biopython/2010-June/006598.html

* I'm representing intron locations relative to CDS coords using the
HGVS standards: http://www.hgvs.org/mutnomen/refseq_figure.html
I'd like to know if there are other common ways of representing such positions.

* In order to customize the display of positions (e.g. 0-based or
1-based), I'm using a class as a configuration container. I've read on
StackOverflow that attempts to use globals or a singleton class are
discouraged in Python, but I have not found practical suggestions for
how to implement module-wide configurations. Suggestions are welcome.

* Any advice about circular genomes or strandedness is also welcome.

* This mapper will work for SeqRecords, SeqFeatures, FeatureLocations,
etc. Are there other Biopython objects that store sequence coordinates
and thus should be mappable?

Regards,

Lenna