I have a sequence file seq.txt which gives each sequence of length 150bp at the specific position. 
seq.txt

position    range    seq
46    1..1524    -----------------
832    1..1524    -----------------
1008    1..1524    -----------------
1407    1..1524    -----------------
2360    2052..3260    ------------------
2967    2052..3260    ------------------
403    1..1524    -----------------
800    1..1524    -----------------
2986    2052..3260    ------------------
3170    2052..3260    ------------------

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I want to find out how much sequence is covered within a particular range. For example range 1...1524 is reported with 6 positions 46, 403, 800, 832, 1008, 1407 where there is an overlap between 800 and 832. The output should give (150+150+32+118+32+150+150) = 782 With my script I am trying to create an array which stores 1 to 1524. Making the array 1 if it contains the position+150 else the array is set to 0. But there is a problem with the loop I think which is not giving the correct output. Any help or idea will be appreciated. My script is: 

use strict;
use warnings;
my $i;
my $j;
my $seq;

open my $m, '<', 'count_try.txt' or die 'Cannot open count_try.txt';
while ($seq = <$m>) {
    chomp $seq;
    
        my (@range) = split(/\t/, $seq);
        my ($fm, $to) = split(/\.\./, $range[1]);

my $r = $range[0];
        for ($i = $fm; $i <= $to; $i++)
{ $j = $r + 150;
if ($i >= $r and $i <= $j)
{$range[$i] = 1;}
else
{$range[$i] = 0;}
print $range[$i]."\t";
}

    
}
close $m;

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In reply to find the coverage of sequence in a particular range by Anonymous Monk

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