here is what I have and as I said it didn't work with the data format I am working with:

#!/usr/bin/perl
use strict;
use integer;

    my $input = shift @ARGV || 'Data.txt'; 
    my $output = shift @ARGV || 'Output.txt'; 
        print $input, "\n";
        open(DATA,"$input") || die "cannot open $input for reading";
        open(OUT, ">$output") || die "cannot open $output for writing"
+;

        my @newcols=();
        my ($genome, $id, $abd);
        my %phage=();
        my @pg=();
        my @id=();

        while (my $line=<DATA>){
            chomp $line;
            #$line =~ s/"//g;
            if($line =~ m/#/){
                $genome = $line;
                          push(@pg, $genome);}
            elsif($line !=~ m/#/){ my @cols = split(/\t/, $line);
                $id = $cols[0];
                $abd = $cols[1];
                          push(@id, $id);
                          $phage{$id}{$genome}=$abd;}
                          
          #print OUT "$genome $id, $abd\n";

        }
        
            my %hash   = map { $_ => 1 } @id;
            my @unique = keys %hash;
            my @sorted_id = sort { ( $a <=> $b) } @unique;
            
            print OUT "\t";    
            for my $phagegenome(@pg){
                print OUT $phagegenome, "\t";
                }
            print OUT "\n";    
            for my $sorted_id(@sorted_id){
                    print OUT $sorted_id, "\t";
                for my $pg(@pg){
                        print OUT "$phage{$sorted_id}{$pg}\t";
                            }
                                print OUT "\n";
            }
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