use strict;
use warnings 'all';
use feature 'say';

my %score;
while (<>) {
    chomp;
    my @row = split /\t/;
    push @{ $score{$row[0]}{$row[1]} }, $row[2], $row[3];
}

my @keys = keys %score;

say join "\t", "", @keys;
for my $key (@keys) {
    say join "\t", $key, map { $score{$key}{$hit} ? $score{$key}{$hit}[0] : ""  } @keys;
}