comparison sum_fastqc.pl @ 7:53bfb3b2c026 draft

Uploaded

6:e386e916efa1

my($inname)=shift(@ARGV);
my($qscore)=shift(@ARGV);
$qscore=~s/\s+//g;
my(@qlist)=split(/\,/,$qscore);

print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\%\tMaxN\%\tMeanLen\tMeanQ";
foreach(@qlist) {
  print "\tQ".$_;
}
print "\n";

foreach (@ARGV) {
  print_stats($_);

   }
   $qmean = sprintf("%.2f", 100 * $sum / $nreads);
   return $qmean;
}

sub readmean {
   $nreads=shift(@_);
   @qarray=@{$_[0]};
   my($sum) = 0;
 

   $readq = sprintf("%.2f", $sum / $nreads);
   return $readq;
}

sub maxn {
   @narray=@{$_[0]};
   my($max_nval)=0;

   foreach $item (@narray) {
     my($plist,$nval)=split(/\t/,$item);
     if($nval>$max_nval) {
       $max_nval=$nval;
     }
   }
   $max_nval = sprintf("%.2f", 100*$max_nval);
   return $max_nval;
}  

sub meanlen {
   $nreads=shift(@_);
   @larray=@{$_[0]};
   my($sum) = 0;

7:53bfb3b2c026

my($inname)=shift(@ARGV);
my($qscore)=shift(@ARGV);
$qscore=~s/\s+//g;
my(@qlist)=split(/\,/,$qscore);

print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\%\tMax_N\%\tAvg_Len\tMean_Q";
foreach(@qlist) {
  print "\tQ".$_."\%";
}
print "\n";

foreach (@ARGV) {
  print_stats($_);

   }
   $qmean = sprintf("%.2f", 100 * $sum / $nreads);
   return $qmean;
}

# Calculate mean read Q score
sub readmean {
   $nreads=shift(@_);
   @qarray=@{$_[0]};
   my($sum) = 0;
 

   $readq = sprintf("%.2f", $sum / $nreads);
   return $readq;
}

# Find position with hights fraction of Ns 
sub maxn {
   @narray=@{$_[0]};
   my($max_nval)=0;

   foreach $item (@narray) {
     my($plist,$nval)=split(/\t/,$item);
     if($nval>$max_nval) {
       $max_nval=$nval;
     }
   }
   $max_nval = sprintf("%.4f", $max_nval);
   return $max_nval;
}  

# Calculate mean read length
sub meanlen {
   $nreads=shift(@_);
   @larray=@{$_[0]};
   my($sum) = 0;