Mercurial > repos > estrain > sum_fastqc

changeset 4:d47775122e78 draft

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Uploaded
author estrain
date Wed, 17 Oct 2018 16:29:11 -0400
parents 8256c1d0d63b
children 7df018757d26
files sum_fastqc.pl
diffstat 1 files changed, 17 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/sum_fastqc.pl	Wed Oct 17 11:10:03 2018 -0400
+++ b/sum_fastqc.pl	Wed Oct 17 16:29:11 2018 -0400
@@ -16,7 +16,7 @@
 $qscore=~s/\s+//g;
 my(@qlist)=split(/\,/,$qscore);
 
-print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC";
+print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\tMeanQ";
 foreach(@qlist) {
   print "\tQ".$_;
 }
@@ -53,7 +53,8 @@
   print $pass[1]."\t";
   print $nreads[1]."\t";
   print $npoor[1]."\t";
-  print $gc[1];
+  print $gc[1]."\t";
+  print readmean($nreads[1],\@qlines);
   foreach $qs (@qlist) {
     print "\t";
     print qcal($nreads[1],$qs,\@qlines);
@@ -77,3 +78,17 @@
    $qmean = sprintf("%.2f", 100 * $sum / $nreads);
    return $qmean;
 }
+
+sub readmean {
+   $nreads=shift(@_);
+   @qarray=@{$_[0]};
+   my($sum) = 0;
+ 
+   foreach $item (@qarray) {
+      my($qval,$q)=split(/\t/,$item);
+      $sum += $q*$qval;
+   }
+
+   $readq = sprintf("%.2f", $sum / $nreads);
+   return $readq;
+}