/usr/share/art-nextgen-simulation-tools/ART_profiler_illumina/summation.pl is in art-nextgen-simulation-tools-profiles 20160605+dfsg-2build1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 | #!/usr/bin/perl
# A perl program to compute the summation of frequency amongst multiple files for each
# quality score.
# @author Jason Myers
use strict;
# Print an error message unless the atleast two fastqReadAvg files and an output file are specified
my $numArgs = $#ARGV + 1;
unless( $numArgs >= 3){
print "Usage: perl summation.pl fastqReadAvg_file1 fastqReadAvg_file2 [fastReadqAvg_fileN] outputFile \n";
exit;
}
# Arrays to hold the different quality score frequencies by base
my @COMB_FREQA = ();
my @COMB_FREQT = ();
my @COMB_FREQG = ();
my @COMB_FREQC = ();
my @COMB_FREQN = ();
# A variable to track the maximum length read seen
my $maxLength = 0;
# Loop over the input files
for(my $iter = 0; $iter < ($numArgs - 1); $iter++){
# Open the file in question
my $infile = $ARGV[$iter];
open INFILE, "$infile", or die $!;
# Set the line counter to 0
my $count = 0;
# An array to temporarily store each files frequency lines
my @TEMP = ();
# A variable to hold the initial grab of the current line
my $line = '';
# variable corresponding to the current length
my $curLength;
# Loop over each line of the file
while(<INFILE>){
if( $count >= 2 && $count <= 73 ){
# get the line
$line = $_;
# set the current length to 0.
$curLength = 0;
# split the line up into its elements
@TEMP = split('\t', $line);
# calculate the current length of read being seen
$curLength = $#TEMP / 5;
# if the current length is longer than the current maximum length seen
# set the max length to the current length
if($curLength > $maxLength){
$maxLength = $curLength;
}
# iterate over the elements of the current line and add them to their corresponging positions
for(my $iter = 0; $iter < 5; $iter++){
for(my $k = 0; $k < $curLength; $k++){
if( $iter == 0){
$COMB_FREQA[($count - 2)][$k] += $TEMP[(($iter * $curLength) + $k)];
} elsif( $iter == 1){
$COMB_FREQT[($count - 2)][$k] += $TEMP[(($iter * $curLength) + $k)];
} elsif( $iter == 2){
$COMB_FREQG[($count - 2)][$k] += $TEMP[(($iter * $curLength) + $k)];
} elsif( $iter == 3){
$COMB_FREQC[($count - 2)][$k] += $TEMP[(($iter * $curLength) + $k)];
} else{
$COMB_FREQN[($count - 2)][$k] += $TEMP[(($iter * $curLength) + $k)];
}
}
}
# set the temp variable back to null
@TEMP = ();
}
# increase the line counter
$count++;
}
# close the current infile
close(INFILE);
}
# open the outfile
my $outfile = $ARGV[$numArgs - 1];
open OUTFILE, ">>$outfile", or die $!;
# set the first base to 'A'
my $base = 'A';
# write the header out to the output file
for( my $iter = 0; $iter < 5; $iter++){
if( $iter == 0){
} elsif( $iter == 1 ){
$base = 'T';
} elsif( $iter == 2 ){
$base = 'G';
} elsif( $iter == 3 ){
$base = 'C';
} else {
$base = 'N';
}
foreach my $pos1 (0 .. ($maxLength - 1)){
print OUTFILE $base, $pos1, "\t";
}
}
print OUTFILE "\n";
# write the contents of each combined frequency array out to the output
# file in the correct order
for(my $i = 0; $i < 71; $i++){
for(my $u = 0; $u < 5; $u++){
for(my $j = 0; $j < $maxLength; $j++){
if($u == 0){
print OUTFILE $COMB_FREQA[$i][$j], "\t"
} elsif($u == 1){
print OUTFILE $COMB_FREQT[$i][$j], "\t"
} elsif($u == 2){
print OUTFILE $COMB_FREQG[$i][$j], "\t"
} elsif($u == 3){
print OUTFILE $COMB_FREQC[$i][$j], "\t"
} else{
print OUTFILE $COMB_FREQN[$i][$j], "\t"
}
}
}
print OUTFILE "\n";
}
# close the output file
close(OUTFILE);
# end summation.pl
exit;
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