#!/usr/bin/perl -w
use strict;
use List::Util 'shuffle';
use List::Util 'shuffle';
#g=generation
#G=Generation
#
 
 my @g0;
 my %allgen;
 my $i;
 my $j;
 
 
 @g0= ("ATTGTACATGTAGTTCTA"); #Initial generation "seeding generation"
 
 %allgen=(0 =>\@g0);
 
        for($i=1;$i<20;$i++) # This $i determines the number of replications 
        {
           my @new_gen=();
           my @last_gen=@{$allgen{$i-1}};
         
            foreach my $seq_string(@last_gen)
            {
                chomp $seq_string;
                
                my @nucleotide_array = split(//,$seq_string);
		my $rand_virus=(int rand(0+10)); # this will randomly select a number of viruses that will seed the new generation from the pool of the last generation
               for($j=0;$j<$rand_virus;$j++) #This loop should allow only $rand_virus sequnces from the new generation to be selected for"multiplying" 
                {
                    my $new_string;
                            
                    foreach my $nucleotide(@nucleotide_array)
                    {
                        chomp $nucleotide;
                                
                        my($T,$G,$C,$A);
                        #These mutations rates are just for testing now they dont reflect accurate viral mutation rates yet
                            if ($nucleotide eq 'A'){
                                   # $T=.1;$G=.2;$C=.3;$A=.7;
                                    my $score = (int rand(0+1000))/1000;
                                    if( $score>=000 && $score<=.099){ $nucleotide=~s/A/T/g;}                       
                                    if( $score>=.100 && $score<=.199){ $nucleotide=~s/A/G/g;} 
                                    if( $score>=.200 && $score<=.299){ $nucleotide=~s/A/C/g;} 
                                   # if( $score>=.300 && $score<=1.00){  Do NOTHING      } }
                                }
                            elsif ($nucleotide eq 'T'){
                                   # $A=.1;$G=.2;$C=.3;$T=.7;
                                    my $score = (int rand(0+1000))/1000;
                                    if( $score>=0 && $score<=.099){ $nucleotide=~s/T/A/g;}                       
                                    if( $score>=.100 && $score<=.199){ $nucleotide=~s/T/G/g;} 
                                    if( $score>=.200 && $score<=.299){ $nucleotide=~s/T/C/g;} 
                                    #if( $score>=.300 && $score<=1.00){  DO NOTHING      } }
                                }
                            elsif ($nucleotide eq 'C'){
                                   # $T=.1;$G=.2;$A=.3;$C=.7;
                                    my $score = (int rand(0+1000))/1000;
                                    if( $score>=0 && $score<=.099){ $nucleotide=~s/C/T/g;}                       
                                    if( $score>=.100 && $score<=.199){ $nucleotide=~s/C/G/g;} 
                                    if( $score>=.200 && $score<=.299){ $nucleotide=~s/C/A/g;} 
                                    #if( $score>=.300 && $score<=1.00){  #No mutation} 
                                }
                            elsif ($nucleotide eq 'G'){
                                   # $T=.1;$A=.2;$C=.3;$G=.7;
                                    my $score = (int rand(0+1000))/1000;
                                    if( $score>=0 && $score<=.099){ $nucleotide=~s/G/T/g;}                       
                                    if( $score>=.100 && $score<=.199){ $nucleotide=~s/G/A/g;} 
                                    if( $score>=.200 && $score<=.299){ $nucleotide=~s/G/C/g;} 
                                    #if( $score>=.300 && $score<=1.00){  #No mutation} 
                                }
                        $new_string= $new_string . $nucleotide;
                    }
                    push(@new_gen,$new_string);
                }         
            }       
            
        @new_gen=shuffle(@new_gen);
           
        #print $allgen{0}[0] . "\n";
         
         $allgen{$i}=\@new_gen;
        }
           
         for my $ii(0..20){
            for (my $jj=0;$jj<(length($jj));$jj++){
                print "$ii\t$allgen{$ii}[$jj] \n";
            }
        }