Hi everyone! First of all, I'm sorry for my English, I'm not mothertongue and I hope what I will write is understandable. I'm writing you for an help: I'm studying for the first time in my life bioinformatics and Perl and I wrote this program but there are two things I can't do. Could you help me? Here it is my program:

 #!/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";
}
[download]

First, I don't know how I could write my output in order to still have a fastq format, written in a file and not on the screen. Then, I'm not so conveinced about my output... printed sequences have the same lenght. Maybe there is a problem in the sliding window operation but I don't know where it is. I know if I start with + = good and - = bad, my result should be: +++--++ input +++ output and not +++--++ input +++++ output I don't know how I could stop at the first "bad" window... Could you help me? Thanks a lot Artu5

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