Using toolic's code from Statistics on Tab Delimited File, I was able to adapt to what you seem to want. 
use strict;
use warnings;
use Acme::Tools;
use Text::Table;

my %data;
my %freq;

while (<DATA>) {
    my ($organism, @vals) = (split)[2..5];
    $freq{ $organism }++;
    my $col = 3;
    for my $val (@vals) {
        push @{ $data{$organism}{$col} }, $val;
        $col++;
    }
}

my @headers =  qw/ Organism Frequency Median_Eval Median_Contig_Length
+ Median_Mapped_Length /;

my $tb = Text::Table->new( map {title => $_}, @headers );

for my $test (sort {$freq{ $b } <=> $freq{ $a }} keys %freq) {
    my @row = ($test, $freq{ $test });
    for my $col (sort keys %{ $data{$test} }) {
        push @row, median(@{ $data{$test}{$col} });
    }
    $tb->load( [@row] );
}
print $tb;
__DATA__
contig1 AC344 organism1 1e-1 122 45
contig1 AC344 organism1 1e-2 122 45
contig1 AC346 organism2 1e-102 122 46
contig1 Ac346 organism2 1e-100 122 46
contig1 Ac346 organism2 1e-114 122 46
contig1 Ac346 organism2 1e-111 122 46
contig2 NC333 organism3 1e-2 155 90
contig3 NC444 organism4 1 188 50
contig3 NC444 organism4 12 188 50

[download]
Output was 
C:\perlp>812293.pl
Organism  Frequency Median_Eval      Median_Contig_Length Median_Mappe
+d_Length
organism2 4         5.000000005e-103 122                  46
organism1 2         0.055            122                  45
organism4 2         6.5              188                  50
organism3 1         1e-2             155                  90

[download]
Is this what you were looking for?

Chris

In reply to Re: Statistics via hash- NCBI BLAST Tab Delimited file by Anonymous Monk
in thread Statistics via hash- NCBI BLAST Tab Delimited file by Paragod28

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