Mercurial > repos > estrain > sum_fastqc
annotate sum_fastqc.pl @ 7:53bfb3b2c026 draft
Uploaded
author | estrain |
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date | Thu, 18 Oct 2018 22:04:04 -0400 |
parents | 7df018757d26 |
children | 5a9a44e23dad |
rev | line source |
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3 | 1 #!/usr/bin/perl |
2 | |
3 #################################################### | |
4 ## | |
5 ## sum_fastqc.pl | |
6 ## | |
7 ## Errol Strain (estrain@gmail.com) | |
8 ## | |
9 ## Description: Takes raw FASTQC output and produces | |
10 ## simple table summary | |
11 ## | |
12 #################################################### | |
13 | |
14 my($inname)=shift(@ARGV); | |
15 my($qscore)=shift(@ARGV); | |
16 $qscore=~s/\s+//g; | |
17 my(@qlist)=split(/\,/,$qscore); | |
18 | |
7 | 19 print "Input\tFile\tFastQC\tPass-Fail\tReads\tPoor_Reads\tGC\%\tMax_N\%\tAvg_Len\tMean_Q"; |
3 | 20 foreach(@qlist) { |
7 | 21 print "\tQ".$_."\%"; |
3 | 22 } |
23 print "\n"; | |
24 | |
25 foreach (@ARGV) { | |
26 print_stats($_); | |
27 } | |
28 | |
29 sub print_stats { | |
30 $infile = shift; | |
31 # First 10 lines of raw FASTQC contain basic overview | |
32 @sumlines=`head -n 10 $infile`; | |
33 chomp(@sumlines); | |
34 | |
35 # Sequence level Q scores are buried in the middle of the file | |
36 @qlines=`awk '/#Quality\tCount/,/>>END_MODULE/' $infile | head -n -1 | tail -n +2`; | |
37 chomp(@qlines); | |
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 |
3 | 45 @fastqc = split(/[\n\t]/,shift(@sumlines)); |
46 @pass = split(/\t/,shift(@sumlines)); | |
47 shift(@sumlines); | |
48 @fn = split(/\t/,shift(@sumlines)); | |
49 shift(@sumlines); | |
50 shift(@sumlines); | |
51 @nreads = split(/\t/,shift(@sumlines)); | |
52 @npoor = split(/\t/,shift(@sumlines)); | |
53 shift(@sumlines); | |
54 @gc = split(/\t/,shift(@sumlines)); | |
55 | |
56 print $inname."\t"; | |
57 print $fn[1]."\t"; | |
58 print $fastqc[1]."\t"; | |
59 print $pass[1]."\t"; | |
60 print $nreads[1]."\t"; | |
61 print $npoor[1]."\t"; | |
4 | 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"; |
4 | 65 print readmean($nreads[1],\@qlines); |
3 | 66 foreach $qs (@qlist) { |
67 print "\t"; | |
68 print qcal($nreads[1],$qs,\@qlines); | |
69 } | |
70 print "\n"; | |
71 } | |
72 | |
73 # Sum reads w/ Q scores > cutoff and divide by number of reads | |
74 sub qcal { | |
75 $nreads=shift(@_); | |
76 $cutoff=shift(@_); | |
77 @qarray=@{$_[0]}; | |
78 $sum = 0; | |
79 | |
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 } |
3 | 85 } |
86 $qmean = sprintf("%.2f", 100 * $sum / $nreads); | |
87 return $qmean; | |
88 } | |
4 | 89 |
7 | 90 # Calculate mean read Q score |
4 | 91 sub readmean { |
92 $nreads=shift(@_); | |
93 @qarray=@{$_[0]}; | |
94 my($sum) = 0; | |
95 | |
96 foreach $item (@qarray) { | |
97 my($qval,$q)=split(/\t/,$item); | |
98 $sum += $q*$qval; | |
99 } | |
100 | |
101 $readq = sprintf("%.2f", $sum / $nreads); | |
102 return $readq; | |
103 } | |
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104 |
7 | 105 # Find position with hights fraction of Ns |
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106 sub maxn { |
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107 @narray=@{$_[0]}; |
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108 my($max_nval)=0; |
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109 |
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110 foreach $item (@narray) { |
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111 my($plist,$nval)=split(/\t/,$item); |
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112 if($nval>$max_nval) { |
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113 $max_nval=$nval; |
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114 } |
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115 } |
7 | 116 $max_nval = sprintf("%.4f", $max_nval); |
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117 return $max_nval; |
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118 } |
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119 |
7 | 120 # Calculate mean read length |
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121 sub meanlen { |
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122 $nreads=shift(@_); |
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123 @larray=@{$_[0]}; |
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124 my($sum) = 0; |
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125 |
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126 foreach $item (@larray) { |
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127 my($lenrange,$count)=split(/\t/,$item); |
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128 my($l1,$l2)=split(/\-/,$lenrange); |
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129 $sum+=(($l1+$l2)/2)*$count; |
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130 } |
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131 $sum = sprintf("%.1f",$sum/$nreads); |
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132 return $sum; |
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133 } |