use strict;
use Data::Dumper; # for investigating data structures

my %data;   # load data into hash of arrays
while (<DATA>)
{
    chomp;
    my @fields = split/,/;
    $data{$fields[0]} = \@fields; # first column = hash key
}
print "\%data - \n", Dumper(\%data);

# We will transform the hash into a sorted array
# sorted on the 3rd column (score)
my @array = sort { $a->[2] <=> $b->[2] } map { $data{$_} } keys %data;
print "\@array - \n", Dumper(\@array);

# Output sorted data lines
print "Sorted data - \n";
foreach (@array)
{
	printf "%s\n", join ',', @{$_};
}

__DATA__
Sequence1,0001,80
Sequence2,0002,20
Sequence3,0003,40
Sequence4,0004,100
Sequence5,0005,70