Hi all!
I have a 2 columns file (position, value) and I want to create a sliding window of 10000 and calculate the average for each window.
My data is

position  value
12498248  1.033560
12512575  0.566400
12513687      0.632940
12520106      0.232530
12523984      0.247300
12525383  1.487640

[download]

So far, I tried this code...but it doesn't work..

#!usr/bin/perl

use warnings;
use strict;
use List::Util 'sum'; 

print '
###############
Establish windows of 10kb and calculate the average Recomb Rate
###############
';

my $recomb_all = $ARGV[0];

my @recomb_all = @{get_contents ($recomb_all)};

#Testing content
print "line 1 column 2 ::: $recomb_all[0][1]\n";

my $length = (scalar @recomb_all) - 1;


my @window;
my $window_size = 10000;
my $window_step = 10000;
my @average;
for (my $i = 0; ($i + $window_size - $window_step) <= $recomb_all[$len
+gth][0]; $i += $window_step) {
    my $e = $i + $window_size;
    if ($e > $recomb_all[$length][0]) {
        $e = $recomb_all[$length][0];
        push (@window, $recomb_all[$length][1]);
        print "@window\n";
        push (@average, $recomb_all[$length][0], my $av = average (@wi
+ndow));
    }    
}
        
#print "@window\n";
#print "@average\n";

exit;

#######################
#SUBROUTINES
#######################


sub get_contents {
    my    ( $file )    = @_;
    my @contents;
    open (FH, "< $file") or die "I cannot open $file file: $!\n";
    my $x = 0;
    while (<FH>) {
        next unless /\S/;
        next if /^\s*[A-Z]+/i;
        @{$contents[$x]} = split /\s+/;
        ++$x;
    }
       
    return (\@contents);
}    # ----------  end of subroutine get_contents  ----------

sub average {
    my @array = @_;
    return sum(@array) / @array;
}

[download]

I would really appreciate any help! Thanks!

In reply to calculate average in sliding windows by marfabe

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