Hi! :) I'm new here and I'm also at my first approaches to Bioinformatics. I found this Perl script and I don't really understand all the passages, in particular in the end. Could someone explain me it, maybe telling me why programmers used these ways to write the script and not others? I know maybe this is not a real good question but I'd really like to understand this script and I don't know how to do it... I have already search for the meanings of the different features in the manual but I can't understand why some of them have been applied here... Thank you very much and I hope you could understand my English!

Update: crossposted here http://www.biostars.org/p/297182/

        $file=shift;

        print "Window length\n";
        $kmer=<STDIN>;
        chomp ($kmer);

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

         open (MYFILE, ">R.txt");   

         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(@qual);                                   
+              
                    }else{
                        last;
                    }   
                }
                $sub1=substr($dna,-$#qual);
                $sub11=substr($qual,-$#qual);

                @qscopy=reverse @num_value;
                foreach $value (@qscopy) 
                {
                    if ($value<$cut_off){
                        pop(@qual); 
                    }else{
                        last;                           
                    }
                }
                $sub2=substr($sub1,0,$#qual);
                $sub22=substr($sub11,0,$#qual);

                for ($i=0;$i<=$#qual-($kmer-1);$i++)
                {
                    @scores=@num_value[$i..$i+$kmer-1];

                    $sum=0;
                    foreach $score (@scores)
                    {
                        $sum+=$score;
                    }
                        if (($sum/$kmer)<$cut_off){
                            last;
                        }
                }                               
                $sub3=substr($sub2,0,($i-1));
                $sub33=substr($sub22,0,($i-1));

print MYFILE "$header1$sub3\n$header2$sub33\n\n";
}   
   }else{
print "Error!\n";
   }

  close MYFILE;

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In reply to explanation of passages of a Perl script by uuuiii

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