On Fri, Dec 10, 2010 at 01:04:41PM -0800, Scott wrote:
> Thanks for all the work on pygr, it's very useful tool.
> 
> I am curious why empty sequence intervals aren't allowed.  One use
> case of pygr is to model mutations (snp, insertions, deletions, etc).
> When modeling an insertion it would be useful to treat it as an empty
> sequence interval (hg19['chr7'][location:location] for example).  I
> have a work around in place that ignores the SeqPath bounds check.
> This allows one to get the up and down stream flanking sequence for an
> insertion.  Is there a better way to model insertions with pygr?

Hi Scott,

I think that's a good use case for empty sequence intervals, and one I
ran across myself a few months ago.  I don't know if the NLMSA data
structure can handle this, however; Chris?

--titus
-- 
C. Titus Brown, c...@msu.edu

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