[Numpy-discussion] Overlapping ranges

Robert Kern robert.kern@gmail....
Mon Mar 16 16:29:04 CDT 2009

2009/3/16 Peter Saffrey <pzs@dcs.gla.ac.uk>:

> At the moment, I'm using a fairly naive approach that finds roughly in the
> genome (which gene) each point might be and then checking it against the
> bins in that gene. If I split the problem into chromosomes, I feel sure
> there must be some super-fast matrix approach I can apply using numpy, but
> I'm struggling a bit. Can anybody suggest something?

You probably need something algorithmically better, like interval
trees. There are a couple of C/Python implementations floating around.

Robert Kern

"I have come to believe that the whole world is an enigma, a harmless
enigma that is made terrible by our own mad attempt to interpret it as
though it had an underlying truth."
  -- Umberto Eco

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