my %data;
while (<DATA>) {
    my ($key, $from, $end) = split;
    if (!$data {$key}) {
        $data {$key} = [[$from, $end, 1]];
    }
    else {
        my @new;
        my $count = 1;
        foreach my $segment (@{$data{$key}}) { 
            if ($from < $$segment[1] && $end > $$segment[0]) { 
                #
                # Must overlap, so merge
                #
                $from = $$segment[0] if $$segment[0] < $from;
                $end = $$segment[1] if $$segment[1] > $end; 
                $count += $$segment[2];
            }
            else {
                #
                # No overlap. Keep.
                #
                push @new, $segment;  
            }
        }
        push @new, [$from, $end, $count];  

        $data{$key} = [sort {$$a[0] <=> $$b[0]} @new];
    }
}

foreach my $key (sort keys %data) {
    my @segments = @{$data{$key}};
    for (my $i = 0; $i < @segments; $i++) {
        printf "ID_%d    %s   %d   %d   %d\n", $i + 1, $key, @{$segmen
+ts[$i]};
    }
}
    
__DATA__
chr1    101  105   X     X     -
chr1    102  108   X     X     -
chr1    106  111   X     X     -
chr1    112  113   X     X     -
chr1    113  115   X     X     -
chr2    114  118   X     X     -
chr2    119  121   X     X     -
chr2    120  123   X     X    -
chr3    125  130   X     X    -
chr3    131  132   X     X   -

[download]
As output, I get: 
ID_1    chr1   101   111   3
ID_2    chr1   112   113   1
ID_3    chr1   113   115   1
ID_1    chr2   114   118   1
ID_2    chr2   119   123   2
ID_1    chr3   125   130   1
ID_2    chr3   131   132   1

[download]
Note this has two ranges from chr3; not 1. I don't see anything spanning the gap from 130 to 131 in your input.

In reply to Re: Counting problem! by JavaFan
in thread Help the counting! by g-alone

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