#!/usr/bin/perl 

# quality trimming of fastq file  

print "Write the window length\n";
$kmer=<STDIN>;
chomp ($kmer);

print "Write the minimum quality score cut-off\n";
$cut_off=<STDIN>;
chomp ($cut_off);

$file = "lib-pool-fosmid.fastq";

if (open(FASTQ,$file)) 
{
	while($header1=<FASTQ>)	
	{ 				
		$dna=<FASTQ>; 
		$header2=<FASTQ>; 
		$qual=<FASTQ>; 
	
		@dna=split ('', $dna); 
		@qual=split ('', $qual); 
		@num_value=();
		@scores=();
		
		foreach $qscore (@qual) 
			{
			   $num_value=ord($qscore)-33;
			   push(@num_value, $num_value);
			}
			
		foreach $value (@num_value) 
			{
				if ($value<$cut_off)
				{ 	
					pop(@num_value);													
				}else{
					last;
				}	
			}
		$sub1=substr($dna,-@num_value); 
		
		@qscopy=reverse @num_value;
		
		foreach $value (@qscopy) 
			{
				if ($value<$cut_off)
				{
					pop(@qscopy); 
				}else{
					last;							
				}
			}
		
		$sub2=substr($sub1,0,@qscopy); 
		@sub2=split('',$sub2);
		
		@qscopy=reverse @qscopy;
		@final_values=();
		
		for ($i=0;$i<@qscopy-($kmer-1);$i=$i+$kmer) 
		{
			@scores=@qscopy[$i..$i+$kmer-1]; 
			$sum=0; 
				foreach $score (@scores)
				{
					$sum+=$score; 
				}
				if (($sum/$kmer)>$cut_off)
				{
					push(@final_values,@sub2[$i..$i+$kmer-1]);		
				}
		}
		
		print "$header1";
		
	foreach $base (@final_values)
	{	
		print "$base";
	}
	if (@final_values != 0){
		print "\n\n";
	}
	}
	
	}else{
	print "Error! Can't find the file\n";
}