annotate sum_fastqc.pl @ 5:7df018757d26 draft

Added additional fields, max %N sites and average length
author estrain
date Thu, 18 Oct 2018 17:14:47 -0400
parents d47775122e78
children 53bfb3b2c026
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1 #!/usr/bin/perl
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2
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3 ####################################################
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4 ##
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5 ## sum_fastqc.pl
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6 ##
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7 ## Errol Strain (estrain@gmail.com)
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8 ##
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9 ## Description: Takes raw FASTQC output and produces
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10 ## simple table summary
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11 ##
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12 ####################################################
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13
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14 my($inname)=shift(@ARGV);
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15 my($qscore)=shift(@ARGV);
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16 $qscore=~s/\s+//g;
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17 my(@qlist)=split(/\,/,$qscore);
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18
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19 print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\%\tMaxN\%\tMeanLen\tMeanQ";
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20 foreach(@qlist) {
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21 print "\tQ".$_;
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22 }
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23 print "\n";
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24
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25 foreach (@ARGV) {
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26 print_stats($_);
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27 }
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28
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29 sub print_stats {
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30 $infile = shift;
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31 # First 10 lines of raw FASTQC contain basic overview
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32 @sumlines=`head -n 10 $infile`;
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33 chomp(@sumlines);
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34
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35 # Sequence level Q scores are buried in the middle of the file
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36 @qlines=`awk '/#Quality\tCount/,/>>END_MODULE/' $infile | head -n -1 | tail -n +2`;
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37 chomp(@qlines);
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38
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39 @nlines=`awk '/#Base\tN\-Count/,/>>END_MODULE/' $infile | head -n -1 | tail -n +2`;
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40 chomp(@nlines);
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41
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42 @lenlines=`awk '/#Length\tCount/,/>>END_MODULE/' $infile | head -n -1 | tail -n +2`;
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43 chomp(@lenlines);
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44
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45 @fastqc = split(/[\n\t]/,shift(@sumlines));
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46 @pass = split(/\t/,shift(@sumlines));
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47 shift(@sumlines);
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48 @fn = split(/\t/,shift(@sumlines));
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49 shift(@sumlines);
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50 shift(@sumlines);
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51 @nreads = split(/\t/,shift(@sumlines));
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52 @npoor = split(/\t/,shift(@sumlines));
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53 shift(@sumlines);
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54 @gc = split(/\t/,shift(@sumlines));
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55
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56 print $inname."\t";
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57 print $fn[1]."\t";
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58 print $fastqc[1]."\t";
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59 print $pass[1]."\t";
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60 print $nreads[1]."\t";
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61 print $npoor[1]."\t";
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62 print $gc[1]."\t";
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63 print maxn(\@nlines)."\t";
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64 print meanlen($nreads[1],\@lenlines)."\t";
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65 print readmean($nreads[1],\@qlines);
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66 foreach $qs (@qlist) {
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67 print "\t";
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68 print qcal($nreads[1],$qs,\@qlines);
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69 }
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70 print "\n";
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71 }
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72
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73 # Sum reads w/ Q scores > cutoff and divide by number of reads
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74 sub qcal {
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75 $nreads=shift(@_);
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76 $cutoff=shift(@_);
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77 @qarray=@{$_[0]};
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78 $sum = 0;
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79
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80 foreach $item (@qarray) {
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81 my($qval,$q)=split(/\t/,$item);
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82 if($qval>=$cutoff) {
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83 $sum += $q;
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84 }
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85 }
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86 $qmean = sprintf("%.2f", 100 * $sum / $nreads);
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87 return $qmean;
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88 }
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89
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90 sub readmean {
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91 $nreads=shift(@_);
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92 @qarray=@{$_[0]};
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93 my($sum) = 0;
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95 foreach $item (@qarray) {
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96 my($qval,$q)=split(/\t/,$item);
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97 $sum += $q*$qval;
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98 }
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99
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100 $readq = sprintf("%.2f", $sum / $nreads);
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101 return $readq;
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102 }
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103
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104 sub maxn {
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105 @narray=@{$_[0]};
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106 my($max_nval)=0;
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107
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108 foreach $item (@narray) {
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109 my($plist,$nval)=split(/\t/,$item);
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110 if($nval>$max_nval) {
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111 $max_nval=$nval;
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112 }
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113 }
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114 $max_nval = sprintf("%.2f", 100*$max_nval);
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115 return $max_nval;
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116 }
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117
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118 sub meanlen {
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119 $nreads=shift(@_);
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120 @larray=@{$_[0]};
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121 my($sum) = 0;
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122
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123 foreach $item (@larray) {
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124 my($lenrange,$count)=split(/\t/,$item);
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125 my($l1,$l2)=split(/\-/,$lenrange);
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126 $sum+=(($l1+$l2)/2)*$count;
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127 }
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128 $sum = sprintf("%.1f",$sum/$nreads);
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129 return $sum;
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130 }