Mercurial > repos > estrain > sum_fastqc

comparison sum_fastqc.pl @ 8:5a9a44e23dad draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author estrain
date Fri, 19 Oct 2018 14:23:35 -0400
parents 53bfb3b2c026
children b3d943bc70ae
comparison
equal deleted inserted replaced
7:53bfb3b2c026 8:5a9a44e23dad
14 my($inname)=shift(@ARGV); 14 my($inname)=shift(@ARGV);
15 my($qscore)=shift(@ARGV); 15 my($qscore)=shift(@ARGV);
16 $qscore=~s/\s+//g; 16 $qscore=~s/\s+//g;
17 my(@qlist)=split(/\,/,$qscore); 17 my(@qlist)=split(/\,/,$qscore);
18 18
19 print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\%\tMax_N\%\tAvg_Len\tMean_Q"; 19 print "Input\tFile\tFastQC\tReads\tGC\%\tAvg_Len\tMax\_N\%\tMean_Q";
20 foreach(@qlist) { 20 foreach(@qlist) {
21 print "\tQ".$_."\%"; 21 print "\tQ".$_."\%";
22 } 22 }
23 print "\n"; 23 print "\n";
24 24
54 @gc = split(/\t/,shift(@sumlines)); 54 @gc = split(/\t/,shift(@sumlines));
55 55
56 print $inname."\t"; 56 print $inname."\t";
57 print $fn[1]."\t"; 57 print $fn[1]."\t";
58 print $fastqc[1]."\t"; 58 print $fastqc[1]."\t";
59 print $pass[1]."\t";
60 print $nreads[1]."\t"; 59 print $nreads[1]."\t";
61 print $npoor[1]."\t";
62 print $gc[1]."\t"; 60 print $gc[1]."\t";
61 print meanlen($nreads[1],\@lenlines)."\t";
63 print maxn(\@nlines)."\t"; 62 print maxn(\@nlines)."\t";
64 print meanlen($nreads[1],\@lenlines)."\t";
65 print readmean($nreads[1],\@qlines); 63 print readmean($nreads[1],\@qlines);
66 foreach $qs (@qlist) { 64 foreach $qs (@qlist) {
67 print "\t"; 65 print "\t";
68 print qcal($nreads[1],$qs,\@qlines); 66 print qcal($nreads[1],$qs,\@qlines);
69 } 67 }