Thanks for the replies. I obviously didn't describe what I'm trying to accomplish sufficiently well, so let me try again.

These are actually huge 1000 Genomes files, which I want to do population genetics analysis on using bioperl Bio::PopGen modules. But rather than passing an entire chromosome to get the statistics from (which I have already done: it works but the results are not genetically relevant), I want to process 100 kilobase windows sequentially and get separate statistics for each window.

So I am trying to split my data up accordingly. The particular file that I gave a sample of starts at coordinate (i.e. DNA base) number 16,287,215. Only variant bases are listed in the files; this is why there are large gaps between coordinates. I want to start my windows from '1' (as in general, coordinates will vary for different chromosomes), so in this case windows 0 to 161 will be empty, but this doesn't matter as I simply won't pass empty windows to bioperl for analysis. I was imagining that my data would look something like this:

$data{HG00553}[ [], [], [], ...., [0 0,0 0,0 0,0 0,0 0,0 0,0 0,....], 
+[], [], etc.]
$data{HG00554}[ [], [], [], ...., [0 0,0 0,0 0,0 0,0 0,0 0,0 0,....], 
+[], [], etc.]

[download]

..where the pairs of zeros here would be in array number 162 (still comma-delimited), and the following arrays would also be populated (with data not given in the tiny sample I show), but the earlier arrays would be empty in this specific case. It seems to me that a hash of arrays of arrays would be the best way to go about this, but please correct me if this is wrong.

Then subsequently I can pass a particular window number for all individuals to the popgen module to get my stats for that genomic region, then do this for all windows and for each chromosome.

I hope this clarifies what I'm trying to do, and further help would be great! Thanks again.

In reply to Re: Population of HoAoA based on file contents by iangibson
in thread Population of HoAoA based on file contents by iangibson

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