[Chicago] Closest Index

[Oren Livne]

Hi Brian,

I would love to! Unfortunately I can never attend on Thursday nights due 
to another obligation. If I ever get the chance I'll let you know. In 
fact I think the discussion should be expanded more generally to python 
problems arising in genetic applications.

Shelia: the data sets are public. The A-array is in each of the files of 
http://hapmap.ncbi.nlm.nih.gov/downloads/recombination/2011-01_phaseII_B37/genetic_map_HapMapII_GRCh37.tar.gz

The B-arrays are the subset of positions on the product 
http://www.affymetrix.com/browse/products.jsp?productId=131532&navMode=34000&navAction=jump&aId=productsNav#1_1
I don't know if they have a public download for their marker list. Or 
maybe the AWS data set has them - look for Affymetrix chip 5.0 or 6.0.

Yes, there would be natural applications for map-reduce parallelization. 
Not this particular task, but other far-more extensive tasks. Would be 
great to discuss in the ChiPy meeting. This is truly a great mailing list.

Oren


On 1/5/2013 10:05 AM, Brian Ray wrote:
> Oren:
>
> Why don't we carve out some time in our next meeting (Thurs) and talk 
> about possible approaches? Are you open to leading that discussion?
>
>
> On Sat, Jan 5, 2013 at 9:26 AM, Oren Livne <livne at uchicago.edu 
> <mailto:livne at uchicago.edu>> wrote:
>
>     Dear Shelia
>
>     These are great questions.
>     A is a set of positions of genetic markers on a chromosome. It is
>     read from an input data file and is sorted.
>     As such, A has no duplicate elements.
>     A's values have variable density along the chromosome. It is not
>     easy to characterize. Can be locally dense.
>     A is used once. However, I have 22 different (A,B) pairs for 22
>     autosomal chromosomes.
>
>     Oren
>
>
>     On 1/5/2013 9:21 AM, sheila miguez wrote:
>
>         I have naive questions.
>
>         How did A get constructed? If an example of integers in A is
>         1,1,2,3,3,3 is it a list of that, or a counter 2,1,3 or something
>         else? What is the distribution of A? When you do the work do
>         you have
>         to construct A every time or will it live around for a while?
>
>
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>
>
> -- 
> Brian Ray
> @brianray
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>
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