sum_fastqc: sum_fastqc.pl annotate

annotate sum_fastqc.pl @ 7:53bfb3b2c026 draft

Uploaded

author	estrain
date	Thu, 18 Oct 2018 22:04:04 -0400
parents	7df018757d26
children	5a9a44e23dad

rev	line source
3 8256c1d0d63b Uploaded estrain parents: diff changeset	1 #!/usr/bin/perl
8256c1d0d63b Uploaded estrain parents: diff changeset	2
8256c1d0d63b Uploaded estrain parents: diff changeset	3 ####################################################
8256c1d0d63b Uploaded estrain parents: diff changeset	4 ##
8256c1d0d63b Uploaded estrain parents: diff changeset	5 ## sum_fastqc.pl
8256c1d0d63b Uploaded estrain parents: diff changeset	6 ##
8256c1d0d63b Uploaded estrain parents: diff changeset	7 ## Errol Strain (estrain@gmail.com)
8256c1d0d63b Uploaded estrain parents: diff changeset	8 ##
8256c1d0d63b Uploaded estrain parents: diff changeset	9 ## Description: Takes raw FASTQC output and produces
8256c1d0d63b Uploaded estrain parents: diff changeset	10 ## simple table summary
8256c1d0d63b Uploaded estrain parents: diff changeset	11 ##
8256c1d0d63b Uploaded estrain parents: diff changeset	12 ####################################################
8256c1d0d63b Uploaded estrain parents: diff changeset	13
8256c1d0d63b Uploaded estrain parents: diff changeset	14 my($inname)=shift(@ARGV);
8256c1d0d63b Uploaded estrain parents: diff changeset	15 my($qscore)=shift(@ARGV);
8256c1d0d63b Uploaded estrain parents: diff changeset	16 $qscore=~s/\s+//g;
8256c1d0d63b Uploaded estrain parents: diff changeset	17 my(@qlist)=split(/\,/,$qscore);
8256c1d0d63b Uploaded estrain parents: diff changeset	18
7 53bfb3b2c026 Uploaded estrain parents: 5 diff changeset	19 print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\%\tMax_N\%\tAvg_Len\tMean_Q";
3 8256c1d0d63b Uploaded estrain parents: diff changeset	20 foreach(@qlist) {
7 53bfb3b2c026 Uploaded estrain parents: 5 diff changeset	21 print "\tQ".$_."\%";
3 8256c1d0d63b Uploaded estrain parents: diff changeset	22 }
8256c1d0d63b Uploaded estrain parents: diff changeset	23 print "\n";
8256c1d0d63b Uploaded estrain parents: diff changeset	24
8256c1d0d63b Uploaded estrain parents: diff changeset	25 foreach (@ARGV) {
8256c1d0d63b Uploaded estrain parents: diff changeset	26 print_stats($_);
8256c1d0d63b Uploaded estrain parents: diff changeset	27 }
8256c1d0d63b Uploaded estrain parents: diff changeset	28
8256c1d0d63b Uploaded estrain parents: diff changeset	29 sub print_stats {
8256c1d0d63b Uploaded estrain parents: diff changeset	30 $infile = shift;
8256c1d0d63b Uploaded estrain parents: diff changeset	31 # First 10 lines of raw FASTQC contain basic overview
8256c1d0d63b Uploaded estrain parents: diff changeset	32 @sumlines=`head -n 10 $infile`;
8256c1d0d63b Uploaded estrain parents: diff changeset	33 chomp(@sumlines);
8256c1d0d63b Uploaded estrain parents: diff changeset	34
8256c1d0d63b Uploaded estrain parents: diff changeset	35 # Sequence level Q scores are buried in the middle of the file
8256c1d0d63b Uploaded estrain parents: diff changeset	36 @qlines=`awk '/#Quality\tCount/,/>>END_MODULE/' $infile \| head -n -1 \| tail -n +2`;
8256c1d0d63b Uploaded estrain parents: diff changeset	37 chomp(@qlines);
8256c1d0d63b Uploaded estrain parents: diff changeset	38
5 7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	39 @nlines=`awk '/#Base\tN\-Count/,/>>END_MODULE/' $infile \| head -n -1 \| tail -n +2`;
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	40 chomp(@nlines);
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	41
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	42 @lenlines=`awk '/#Length\tCount/,/>>END_MODULE/' $infile \| head -n -1 \| tail -n +2`;
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	43 chomp(@lenlines);
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	44
3 8256c1d0d63b Uploaded estrain parents: diff changeset	45 @fastqc = split(/[\n\t]/,shift(@sumlines));
8256c1d0d63b Uploaded estrain parents: diff changeset	46 @pass = split(/\t/,shift(@sumlines));
8256c1d0d63b Uploaded estrain parents: diff changeset	47 shift(@sumlines);
8256c1d0d63b Uploaded estrain parents: diff changeset	48 @fn = split(/\t/,shift(@sumlines));
8256c1d0d63b Uploaded estrain parents: diff changeset	49 shift(@sumlines);
8256c1d0d63b Uploaded estrain parents: diff changeset	50 shift(@sumlines);
8256c1d0d63b Uploaded estrain parents: diff changeset	51 @nreads = split(/\t/,shift(@sumlines));
8256c1d0d63b Uploaded estrain parents: diff changeset	52 @npoor = split(/\t/,shift(@sumlines));
8256c1d0d63b Uploaded estrain parents: diff changeset	53 shift(@sumlines);
8256c1d0d63b Uploaded estrain parents: diff changeset	54 @gc = split(/\t/,shift(@sumlines));
8256c1d0d63b Uploaded estrain parents: diff changeset	55
8256c1d0d63b Uploaded estrain parents: diff changeset	56 print $inname."\t";
8256c1d0d63b Uploaded estrain parents: diff changeset	57 print $fn[1]."\t";
8256c1d0d63b Uploaded estrain parents: diff changeset	58 print $fastqc[1]."\t";
8256c1d0d63b Uploaded estrain parents: diff changeset	59 print $pass[1]."\t";
8256c1d0d63b Uploaded estrain parents: diff changeset	60 print $nreads[1]."\t";
8256c1d0d63b Uploaded estrain parents: diff changeset	61 print $npoor[1]."\t";
4 d47775122e78 Uploaded estrain parents: 3 diff changeset	62 print $gc[1]."\t";
5 7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	63 print maxn(\@nlines)."\t";
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	64 print meanlen($nreads[1],\@lenlines)."\t";
4 d47775122e78 Uploaded estrain parents: 3 diff changeset	65 print readmean($nreads[1],\@qlines);
3 8256c1d0d63b Uploaded estrain parents: diff changeset	66 foreach $qs (@qlist) {
8256c1d0d63b Uploaded estrain parents: diff changeset	67 print "\t";
8256c1d0d63b Uploaded estrain parents: diff changeset	68 print qcal($nreads[1],$qs,\@qlines);
8256c1d0d63b Uploaded estrain parents: diff changeset	69 }
8256c1d0d63b Uploaded estrain parents: diff changeset	70 print "\n";
8256c1d0d63b Uploaded estrain parents: diff changeset	71 }
8256c1d0d63b Uploaded estrain parents: diff changeset	72
8256c1d0d63b Uploaded estrain parents: diff changeset	73 # Sum reads w/ Q scores > cutoff and divide by number of reads
8256c1d0d63b Uploaded estrain parents: diff changeset	74 sub qcal {
8256c1d0d63b Uploaded estrain parents: diff changeset	75 $nreads=shift(@_);
8256c1d0d63b Uploaded estrain parents: diff changeset	76 $cutoff=shift(@_);
8256c1d0d63b Uploaded estrain parents: diff changeset	77 @qarray=@{$_[0]};
8256c1d0d63b Uploaded estrain parents: diff changeset	78 $sum = 0;
8256c1d0d63b Uploaded estrain parents: diff changeset	79
8256c1d0d63b Uploaded estrain parents: diff changeset	80 foreach $item (@qarray) {
5 7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	81 my($qval,$q)=split(/\t/,$item);
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	82 if($qval>=$cutoff) {
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	83 $sum += $q;
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	84 }
3 8256c1d0d63b Uploaded estrain parents: diff changeset	85 }
8256c1d0d63b Uploaded estrain parents: diff changeset	86 $qmean = sprintf("%.2f", 100 * $sum / $nreads);
8256c1d0d63b Uploaded estrain parents: diff changeset	87 return $qmean;
8256c1d0d63b Uploaded estrain parents: diff changeset	88 }
4 d47775122e78 Uploaded estrain parents: 3 diff changeset	89
7 53bfb3b2c026 Uploaded estrain parents: 5 diff changeset	90 # Calculate mean read Q score
4 d47775122e78 Uploaded estrain parents: 3 diff changeset	91 sub readmean {
d47775122e78 Uploaded estrain parents: 3 diff changeset	92 $nreads=shift(@_);
d47775122e78 Uploaded estrain parents: 3 diff changeset	93 @qarray=@{$_[0]};
d47775122e78 Uploaded estrain parents: 3 diff changeset	94 my($sum) = 0;
d47775122e78 Uploaded estrain parents: 3 diff changeset	95
d47775122e78 Uploaded estrain parents: 3 diff changeset	96 foreach $item (@qarray) {
d47775122e78 Uploaded estrain parents: 3 diff changeset	97 my($qval,$q)=split(/\t/,$item);
d47775122e78 Uploaded estrain parents: 3 diff changeset	98 $sum += $q*$qval;
d47775122e78 Uploaded estrain parents: 3 diff changeset	99 }
d47775122e78 Uploaded estrain parents: 3 diff changeset	100
d47775122e78 Uploaded estrain parents: 3 diff changeset	101 $readq = sprintf("%.2f", $sum / $nreads);
d47775122e78 Uploaded estrain parents: 3 diff changeset	102 return $readq;
d47775122e78 Uploaded estrain parents: 3 diff changeset	103 }
5 7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	104
7 53bfb3b2c026 Uploaded estrain parents: 5 diff changeset	105 # Find position with hights fraction of Ns
5 7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	106 sub maxn {
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	107 @narray=@{$_[0]};
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	108 my($max_nval)=0;
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	109
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	110 foreach $item (@narray) {
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	111 my($plist,$nval)=split(/\t/,$item);
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	112 if($nval>$max_nval) {
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	113 $max_nval=$nval;
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	114 }
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	115 }
7 53bfb3b2c026 Uploaded estrain parents: 5 diff changeset	116 $max_nval = sprintf("%.4f", $max_nval);
5 7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	117 return $max_nval;
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	118 }
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	119
7 53bfb3b2c026 Uploaded estrain parents: 5 diff changeset	120 # Calculate mean read length
5 7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	121 sub meanlen {
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	122 $nreads=shift(@_);
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	123 @larray=@{$_[0]};
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	124 my($sum) = 0;
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	125
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	126 foreach $item (@larray) {
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	127 my($lenrange,$count)=split(/\t/,$item);
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	128 my($l1,$l2)=split(/\-/,$lenrange);
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	129 $sum+=(($l1+$l2)/2)*$count;
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	130 }
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	131 $sum = sprintf("%.1f",$sum/$nreads);
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	132 return $sum;
7df018757d26 Added additional fields, max %N sites and average length estrain parents: 4 diff changeset	133 }

Mercurial > repos > estrain > sum_fastqc

annotate sum_fastqc.pl @ 7:53bfb3b2c026 draft