hello this is my first post. I think third column has some special meaning which I don't know. If treat rows with each third column value, how about like this?

use strict;
use warnings;

my @key=("key", "start", "end");
my @data=();
my $key_pre=0;

while(<DATA>) {
    my %hash;
    @hash{@key}=(split(/,/,$_))[2 .. 4];    #(key=>1, start=>23, end=>
+45)
    if ($key_pre != $hash{key} ){
        &proc_eachkey( \@data ) if $#data > 0;
        @data=();
    }
    $key_pre=$hash{key};
    push @data, {%hash};                    #copy hash value
}
&proc_eachkey( \@data ) if $#data > 0;      #for last key

sub proc_eachkey {
    my ($data)= @_;
    my ($start_pre, $end_pre)=(0,0);

    foreach my $h (@$data){
        if ($end_pre != $h->{start} + 1) {
            printf "%d,%d,%d\n",  $h->{key}, ($start_pre + 1), ($h->{s
+tart} -1);
        }
        printf "%d,%d,%d\n",  $h->{key}, $h->{start}, $h->{end};

        ($start_pre, $end_pre)=($h->{start}, $h->{end});
    }
}
__DATA__
1,34,1,23,45,2,2
35,45,1,56,78,1,1
46,56,1,88,101,2,2
57,68,2,13,34,4,3
69,78,2,45,56,1,3
[download]

nothing better than ikegami's one. regards.