I am attempting to parse a text delimited file that contains sequence data and find the median on each column per organism. I posted a few days ago but I have still been working on an appropriate solution. Toolic helped me last time and I appreciate it but I still seem to be lost. Toolic did create a working solution but I still needed frequency and the proper format via organism. Thanks again for any help. http://www.perlmonks.org/?node_id=812285

Here is an example of my input 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

The first two columns are correct but it breaks apart when I try to get the medians. Here is an example of my output so far:

Organism Frequency Median_Eval Median_Contig_Length Median_Mapped_Length
organism3: 1 ARRAY(0x2838664) 0
organism1: 2 ARRAY(0x2cc2e4) 0
organism4: 2 ARRAY(0x28386b4) 0
organism2: 4 ARRAY(0x27d11ec) 0

Here is my code so far:

use strict;
use warnings;


use Acme::Tools;

my (%count, %organisms, %med, %number);
my $ref_filelist = $ARGV[0];
my ($contig, $accession, $organism, $eval, $con_length, $map_length);
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>){
      
( $contig, $accession, $organism, $eval, $con_length, $map_length ) = 
+split ( '\t',);

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

#$organisms{$organism} = $eval;

my $number = ++$count{$organism};
$number{$organism} = $number;

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

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In reply to Statistics via hash- NCBI BLAST Tab Delimited file by Paragod28

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