Your code prints out <c>$organisms{$organism}

@_=qw;
Just another Perl hacker,;
;$_=q=print
"@_"= and eval;
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    my $med = median(@{$organisms{$organism}});  #bad form, masks %med
+ declared in outer scope. Use a different name for this variable, eg.
+ $med_calculated.
    $med{$organism} = $med;
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foreach $organism (sort {$number{$a} <=> $number{$b}} keys %organisms)
+{
    print "$organism:\t$number{$organism}\t$organisms{$organism}\t$med
+{$organism}\n" ;
}
[download]

use strict;
use warnings;

use Acme::Tools;

my (%count, %organisms, %med, %number);
my ($contig, $accession, $organism, $eval, $con_length, $map_length);

#my $ref_filelist = $ARGV[0];
#open(FILELIST, $ref_filelist )
#   or die "Could not open Reference filelist...($!)";
 
print "Organism\tFrequency\tMedian_Eval\tMedian_Contig_Length\tMedian_
+Mapped_Length\n"; 

#while (<FILELIST>){
while (<DATA>){
    ( $contig, $accession, $organism, $eval, $con_length, $map_length 
+) = split ( '\t',);

    #my $median = $eval[($#eval / 2)];
    my $med_calculated = median(@{$organisms{$organism}});  
    $med{$organism} = $med_calculated;

    #$organisms{$organism} = $eval;
    my $number_calculated = ++$count{$organism};    
    $number{$organism} = $number_calculated;
}

foreach $organism (sort {$number{$a} <=> $number{$b}} keys %organisms)
+{
    print "$organism:\t$number{$organism}\t$organisms{$organism}\t$med
+{$organism}\n" ;
}


__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]

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
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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]

Chris

That is exactly what I was trying to do. Now that I look over my attempt I can see some of the mistakes you all have pointed out. I appreciate the help from all of you monks. I will go through the examples so I can understand the code behind it. I may have some more questions on just exactly why certain things were done. Thank you all!

I noticed 2 changes that should be made.

while (<DATA>) {
    chomp;
    my ($organism, @vals) = (split /\t/)[2..5];
    $freq{ $organism }++;
[download]

The line sfter the read needs to be chomped. And, the split should occur on tabs, not on whitespace. (When I ran the test program above, I split on whitespace instead of tabs because the sample data I copied into the program was separated by spaces, not tabs).

As long as $organism itself doesn't contain spaces you could split on whitespace. But I don't know enough about your data.

Chris

Yes I caught that. My data does have whitespace in the organism column. Thanks. I have been trying to work through the code and have another question. How can I add column 2(text) of the original data to the output and keep it referenced to organism?

Yes you are correct Chris. I was having difficulty keeping column 2(accession) referenced to column 3(organism). I understand the code as the values are pushed into the array but I did not understand how to keep the above referenced to each other. I assume a hash but I was not sure how to implement it along with the other hashes. I was also having a problem with the organism names being too long. I came up with a solution for both. I would rather learn than be given a solution so let me know if this is acceptable practice. Again, thanks for your help.

use strict;
use warnings;
use Acme::Tools;
use Text::Table;

my %data;
my %freq;
my $ref_filelist = $ARGV[0];
open(BLASTFILE, $ref_filelist )
   or die "Could not open Reference filelist...($!)";
   
while (<BLASTFILE>) {
    chomp;
    
    my ($accession,$organism, @vals) = (split /\t/)[1..5];
    my $organismcut = substr( $organism, 0,75 );
    my $tot =$accession . $organismcut;
    #print "$tot\n";
    
    $freq{ $tot }++;
    
    my $col = 4;
    for my $val (@vals) {
        push @{ $data{$tot} {$col} }, $val;
        $col++;
    }
}

my @headers =  qw/ Organism Freq Median_Eval Med_Contig_Length Med_Map
+ped_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 "@row\n"; 
    
}
print $tb;
[download]