If you wanted them back into their original order, you have another step to make.

#! perl -slw
use strict;

my @data =  map{ chomp; [ split '\s*\|\s*', $_ ] } <DATA>;

my @counts;
for my $field ( 1 .. 3 ) {
    my $rank = 0;
    @data = map { 
        $_->[ $field ] and $_->[ $field ] = ++$rank; 
        $_; 
    } sort { 
        ( $a->[ $field ]||0 ) <=> ( $b->[ $field ]||0 ) 
    } @data;
    $counts[ $field ] = $rank;
}

for my $data ( @data ) {
    map {
        $data->[ $_ ] and $data->[ $_ ] 
            = sprintf '%5.3f', $data->[ $_ ] /= $counts[ $_ ];
    } 1 .. 3;
}
print join "\t", @$_ for @data;

__DATA__
ENSG00000179050 |             |               |           4 
ENSG00000124183 |         237 |               |           2 
ENSG00000179033 |             |               |           7 
ENSG00000124181 |             |           13  |           1 
ENSG00000174306 |             |               |           5 
ENSG00000132793 |             |               |           8 
ENSG00000183798 |             |               |           6 
ENSG00000124177 |             |               |           3 
ENSG00000087530 |         153 |               |             
ENSG00000185513 |         258 |               |             
ENSG00000101052 |         231 |               |             
ENSG00000124249 |         154 |             7 |             
ENSG00000101098 |         159 |               |             
ENSG00000166913 |         141 |               |             
__OUTPUT__
P:\test>383173
ENSG00000166913 0.143
ENSG00000087530 0.286
ENSG00000101098 0.571
ENSG00000101052 0.714
ENSG00000185513 1.000
ENSG00000124249 0.429   0.500
ENSG00000124181         1.000   0.125
ENSG00000124183 0.857           0.250
ENSG00000124177                 0.375
ENSG00000179050                 0.500
ENSG00000174306                 0.625
ENSG00000183798                 0.750
ENSG00000179033                 0.875
ENSG00000132793                 1.000
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