contigA 4 5 0 1
contigB 10 1 1 0
etc.

##</code><code>##

#!/usr/bin/perl 

use strict; 
use warnings; 
no warnings qw /syntax/; 

sub zup { 
    join "\n" => map {join " " => map {shift @$_} @_} @{$_ [0]} 
} 

my @array1 = qw /ab bc cd de/; 
my @array2 = qw /cc dd ee gg/; 
my @array3 = qw /12 34 56 78/; 

print zup \(@array1, @array2, @array3); 
print "\n"; 

##</code><code>##

use strict;
use warnings;

my $infile=$ARGV[0];
open (IN,$infile) or die "cannot open $infile";

my %count_Bact; my %count_undef; my %count_ProphVir; my %count_Euk;

while (my $line=<IN>) {
        chomp $line;
        next if ($line =~/^#/) ;
        my ($geneid,$cons_flag)=split(/\t/,$line);
        my @geneid_columns=split(/_/,$geneid);
        my $contig=join("_",$geneid_columns[0],$geneid_columns[1],$geneid_columns[2],$geneid_columns[3]);
        if ($cons_flag eq "Bact"){
                $count_Bact{$contig} ++;
        }
        if ($cons_flag eq "undef"){
                $count_undef{$contig} ++;
        }
        if ($cons_flag eq "Proph_Vir" || $cons_flag eq "Vir" || $cons_flag eq "Proph"){
                $count_ProphVir{$contig} ++;
        }
        if ($cons_flag eq "Euk"){
                $count_Euk{$Euk} ++ ;
        }
}
close (IN);