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Changeset 5:7df018757d26 (2018-10-18)

Previous changeset 4:d47775122e78 (2018-10-17) Next changeset 6:e386e916efa1 (2018-10-18)

Commit message:
Added additional fields, max %N sites and average length

modified:
sum_fastqc.pl

diff -r d47775122e78 -r 7df018757d26 sum_fastqc.pl
--- a/sum_fastqc.pl Wed Oct 17 16:29:11 2018 -0400
+++ b/sum_fastqc.pl Thu Oct 18 17:14:47 2018 -0400

[

@@ -16,7 +16,7 @@
$qscore=~s/\s+//g;
my(@qlist)=split(/\,/,$qscore);

-print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\tMeanQ";
+print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\%\tMaxN\%\tMeanLen\tMeanQ";
foreach(@qlist) {
   print "\tQ".$_;
}
@@ -36,6 +36,12 @@
   @qlines=`awk '/#Quality\tCount/,/>>END_MODULE/' $infile | head -n -1 | tail -n +2`;
   chomp(@qlines);

+  @nlines=`awk '/#Base\tN\-Count/,/>>END_MODULE/' $infile | head -n -1 | tail -n +2`;
+  chomp(@nlines);
+
+  @lenlines=`awk '/#Length\tCount/,/>>END_MODULE/' $infile | head -n -1 | tail -n +2`;
+  chomp(@lenlines);
+
   @fastqc = split(/[\n\t]/,shift(@sumlines));
   @pass = split(/\t/,shift(@sumlines));
   shift(@sumlines);
@@ -54,6 +60,8 @@
   print $nreads[1]."\t";
   print $npoor[1]."\t";
   print $gc[1]."\t";
+  print maxn(\@nlines)."\t";
+  print meanlen($nreads[1],\@lenlines)."\t";
   print readmean($nreads[1],\@qlines);
   foreach $qs (@qlist) {
     print "\t";
@@ -70,10 +78,10 @@
    $sum = 0;

    foreach $item (@qarray) {
-      my($qval,$q)=split(/\t/,$item);
-      if($qval>=$cutoff) {
-        $sum += $q;
-      }
+     my($qval,$q)=split(/\t/,$item);
+     if($qval>=$cutoff) {
+       $sum += $q;
+     }
    }
    $qmean = sprintf("%.2f", 100 * $sum / $nreads);
    return $qmean;
@@ -92,3 +100,31 @@
    $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;
+
+   foreach $item (@larray) {
+     my($lenrange,$count)=split(/\t/,$item);
+     my($l1,$l2)=split(/\-/,$lenrange);
+     $sum+=(($l1+$l2)/2)*$count;
+   }
+   $sum = sprintf("%.1f",$sum/$nreads);
+   return $sum;
+}