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Re: calculate average in sliding windows

by marfabe (Initiate)
on May 23, 2012 at 13:58 UTC ( #972042=note: print w/ replies, xml ) Need Help??


in reply to calculate average in sliding windows

thanks to all...but I still have problems in the sliding window part
Maybe I didn't explain it ok. What I want is to group the first column of the file in windows of 10 kbases (DNA positions) and calculate the average of column 2 for each window.

BrowserUK and Eliya: your idea works fine but it doesn't take into account the positions in column 1...and I'm stuck trying to use it.
Any idea?
Thanks!


Comment on Re: calculate average in sliding windows
Re^2: calculate average in sliding windows
by Eliya (Vicar) on May 23, 2012 at 14:27 UTC
    but it doesn't take into account the positions in column 1

    Sorry, I'm still not sure what you want (and it's a little diffficult to infer it from code which - as you state - doesn't work).

    Are you saying the positions in column 1 are meant to represent indices in some sparse array, with all unspecified positions (such as 12498249..12512574, etc.) implicitly having a value of zero, or what?

    I think it would help if you could come up with some simplified (but sufficient/complete) sample input (say using a window size of 3) together with the desired output values.

      Thanks Eliya
      Here's the simplified sample set

      position value 1 1 10 3 30 1 40 2 60 2

      And here the output for window size of 30

      1-30 1.666666667 31-60 2

        Ok, thanks.  So maybe like this?

        #!/usr/bin/perl -lw use strict; use constant WINDOW => 30; my $sum = 0; my $n = 0; my $p = WINDOW; while (<DATA>) { my ($pos, $val) = split; if (eof) { # corner case $sum += $val; $n++; } if ($pos > $p or eof) { print $sum / $n if $n > 0; $sum = 0; $n = 0; $p += WINDOW while $pos > $p; } $sum += $val; $n++; } __DATA__ 1 1 10 3 30 1 40 2 60 2

        Output:

        1.66666666666667 2

        (Upd: fixed handling of corner case)

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