#!/usr/bin/perl
use warnings; use strict;
use Getopt::Long;
use List::Util qw(shuffle);
my $k=6;
my $window=31;
my $bins=2*$window+$k;
my %ktc;
my $sequence_fname;
my $wiggle_fname;
my $permute=0;
my $normalize_fname;
my $out='default_out';
GetOptions (
	"o=s" => \$out,
	"s=s" => \$sequence_fname,
	"wig=s" => \$wiggle_fname,
	"n=s" => \$normalize_fname,
	"p=i" => \$permute);

############initialize %ktc
$out=$out.'counts.tab';
my $letters=[ qw(A C G T N) ];
my @words=&combin($letters,$k );
foreach(@words){
	@{$ktc{$_}}= ((0)x$bins) ;
}
##########
##########Load normalization file data
open(NORM,"<$normalize_fname")||die "Cannot open normalization file\n";
my %normalize;
while (<NORM>){
	my @a=split(/\t/,$_);
	$normalize{$a[0]}=$a[1];
}
close NORM;
##########Load position counts
my %counts;
open (CTS,'<',$wiggle_fname)||die "Cannot open wiggle file\n";
my $cur_chr='';
my $pos='';
my $counts='';
while (<CTS>){
	if($_=~/variableStep chrom=(.*?)$/){
		$cur_chr=$1;
		$counts{$cur_chr}={};
	}
	else{
		($pos,$counts)=split(/\t/,$_);
		$counts{$cur_chr}{$pos}=$counts;
	}
}
close CTS;
#######
#########Map counts to orfs
my $test=0;
if(!($permute)){
	open(SEQ,'<',$sequence_fname)||die "Cannot open sequence file\n";
	while (my @line=split (/\t/,<SEQ>)){
		my $ct=0;
		my $start=$line[1];
		if ($start < $line[2]){##Watson Strand
			until ($start > $line[2]-$window){
				for(my $i=0;$i<$bins;++$i){
					if(defined $normalize{$line[3]} && $normalize{$line[3]} > 0 && $counts{$line[0]}{$start-$window+$i}){
						${$ktc{substr($line[4],$ct,$k)}}[$i]+=$counts{$line[0]}{$start-$window+$i}/$normalize{$line[3]};
					}
					else{
						++$test;
					}
				}

				++$start;
				++$ct;
			}
		}
		else{##Crick Strand
			until($start < $line[2]+$window){
				for(my $i=0;$i<$bins;++$i){
					if(defined $normalize{$line[3]} && $normalize{$line[3]} > 0 && $counts{$line[0]}{$start-$window+$i}){
						${$ktc{substr($line[4],$ct,$k)}}[$i]+=$counts{$line[0]}{$start-$window+$i}/$normalize{$line[3]};
					}
					else{
						++$test;
					}
				}
				--$start;
				++$ct;
			}
		}
	}
	foreach my $key(keys %ktc){
		if($key=~/N/){
			next;
		}
		print $key,"\t", "@{$ktc{$key}}\n";
	}
}
else{
	for(my $r=0;$r<$permute;++$r){#for all permutation iterations
		foreach my $key(keys %counts){#for each chromosome
			my @values = shuffle(values %{$counts{$key}});#make a array of values
			$counts{$key}{$_} = shift @values for keys %{$counts{$key}};#permute the values to a read position in the chromosome
		}
		foreach(@words){
			@{$ktc{$_}}= ((0)x$bins) ;
		}
		open(SEQ,'<',$sequence_fname)||die "Cannot open sequence file\n";#open the sequence file
		while (my @line=split (/\t/,<SEQ>)){#for each sequence record the nmer information
			my $ct=0;
			my $start=$line[1];
			if ($start < $line[2]){##Watson Strand
				until ($start > $line[2]-$window){
					for(my $i=0;$i<$bins;++$i){
						if(defined $normalize{$line[3]} && $normalize{$line[3]} > 0 && $counts{$line[0]}{$start-$window+$i}){
							${$ktc{substr($line[4],$ct,$k)}}[$i]+=$counts{$line[0]}{$start-$window+$i}/$normalize{$line[3]};
						}
						else{
							++$test;
						}
					}
					++$start;
					++$ct;
				}
			}
			else{##Crick Strand
				until($start < $line[2]+$window){
					for(my $i=0;$i<$bins;++$i){
						if(defined $normalize{$line[3]} && $normalize{$line[3]} > 0 && $counts{$line[0]}{$start-$window+$i}){
							${$ktc{substr($line[4],$ct,$k)}}[$i]+=$counts{$line[0]}{$start-$window+$i}/$normalize{$line[3]};
						}
						else{
							++$test;
						}
					}
					--$start;
					++$ct;
				}
			}
		}
		close SEQ;
		open(OUT,">>$out")||die "Cannot open $out\n";
		foreach my $key(keys %ktc){
			if($key=~/N/){#skip if the nmer contains an N
				#		$ktc{$key}=((0)x$bins);#reset the hash
				next;
			}
			print OUT $key,"\t","@{$ktc{$key}}\n";#print result
#			$ktc{$key}=((0)x$bins);#reset hash 
		}
		close OUT;
	}
}


sub combin{
	my ($data, $q) = @_;

	return if $q < 1;

	my $results = $data;

	while (--$q) {
		my @new;
		for my $letter (@$data) {
			push @new, map { $letter . $_ } @$results;
		} # end for $letter in @$data

		$results = \@new;
	} # end while --$q is not 0

	return @$results;
} # end ordered_combinations