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

#given a completed pentamer count file, sort pentamers, and consolidate duplicates

my @data;
my @currentPentLine;
my $counter;
my $pent;
my $pentExpected;
my $pentObserved;
my $pentTotal;

#read in input file, capturing pentamers and related info for each
open(FREQ,"<testPentamerCounts.txt") or die "Cannot open FREQ output file\n";

while (<FREQ>) {
        chomp;
        @currentPentLine = split("\t", $_);
        $pent = $currentPentLine[0];
        $pentExpected = $currentPentLine[1];
        $pentObserved = $currentPentLine[2];
        $pentTotal = $currentPentLine[3];

#create array of hashes with data from input file
        $data[$counter]{'pent'} = $pent;
        $data[$counter]{'count'} = $pentObserved;
        $data[$counter]{'prob'} = $pentExpected;
        $data[$counter]{'pentTotal'} = $pentTotal;
        $counter++;
        }
close FREQ;

my $criteria = "pent";
my @sorted_pentamers = sort { $a->{$criteria} cmp $b->{$criteria} } @data;

my %totalProbability;
my $probTotal;

for $probTotal (@sorted_pentamers) {
        if (not exists $totalProbability{$probTotal->{pent}}) {
        $totalProbability{$probTotal->{pent}} = 0;
        }
        $totalProbability{$probTotal->{pent}} += $probTotal->{prob};

}
my %totalCounts;
my $countTotal;

for $countTotal (@sorted_pentamers) {
        if (not exists $totalCounts{$countTotal->{pent}}) {
        $totalCounts{$countTotal->{pent}} = 0;
        }
        $totalCounts{$countTotal->{pent}} += $countTotal->{count};
}

my %totalPentCounts;
my $pentTotal;

for $pentTotal (@sorted_pentamers) {
        if (not exists $totalPentCounts{$pentTotal->{pent}}) {
        $totalPentCounts{$pentTotal->{pent}} = 0;
        }
        $totalPentCounts{$pentTotal->{pent}} += $pentTotal->{pentTotal};
}

my @keysProb = keys %totalProbability;
my @keysTotal = keys %totalCounts;

print @keysProb, "\n";
print @keysTotal, "\n";

#print unique sequences to output file

Is there some way I could access iterate through each pentamer as a key in each of the hashes and print out each value? 

Thanks again!