/usr/share/art-nextgen-simulation-tools/ART_profiler_illumina/fastqReadAvg.pl is in art-nextgen-simulation-tools-profiles 20160605+dfsg-2.
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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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 | #!/usr/bin/perl
# A perl program to retrieve quality scores for each base at a given position
# from a fastq file denoted by the user as a command-line argument.
# @author Jason Myers
use FileHandle;
use strict;
#use warnings;
# Making sure that the correct number of arguments are given by the user and
# that the program displays an accurate message in case the user does not.
my $numArgs = $#ARGV + 1;
unless( $numArgs == 1) {
print "Usage: perl fastqReadAvg.pl FastqFile\n";
exit;
}
# Getting the filename to the file of interest
my $infile = $ARGV[0];
my $fh = FileHandle->new;
# Opening the file to be read into and the file to hold the programs output.
#open INFILE, "$infile", or die $!;
if($infile!~/\.gz$/){
$fh->open ("<$infile") or die $!;
}
else{
$fh->open("zcat $infile|") or die $!;
}
my $outFile = $infile . ".txt";
$outFile =~s/^.*\///;
open OUTFILE, ">>$outFile", or die $!;
# Iterator to determine which line to take from the file.
my $iter = 0;
# variable to switch between the operations associated with the called bases and the quality scores
my $whichLine = 1;
# array to store the current line of called bases
my @BASES = ();
# array to store the current line of quality scores
my @SCORES = ();
# variable to hold initial read of the called bases
my $line1 = '';
# variable to hold initial read of quality scores
my $line2 = '';
# Initializing the main data array that is to be base call at a specific position
# by quality score.
my @data = ();
# Variable holding the number of scores possible (0-39)
my $numScores = 71;
# Variable signifying the number of possible bases (ATGC)
my $numBases = 5;
# Variable holding the largest length of read that is in the file
# initialy 0
my $maxLength = 0;
# The ascII value of '!' in decimal format. Used to normalize quality scores
my $normal = 33;
# Variable associated with the position of 'TGC' base scores in the output file
my $Tpos = 1;
my $Gpos = 2;
my $Cpos = 3;
my $Npos = 4;
# Final data matrix
my @finDat = ();
# Matrix to hold the average scores
my @avgScore = ();
# Array holding the different quality scores
my @allScores = ();
# Fill the array.
for(my $r = 0; $r < $numScores; $r++){
$allScores[$r] = $r;
}
# Main while loop that iterates over the fastq file
#while(<INFILE>) {
while(<$fh>) {
# The lines of interest are the odd lines
if( ($iter % 2) != 0 ) {
# If the current line is a called bases line
if($whichLine){
# read in the line
$line1 = $_;
# remove the new-line character
chomp $line1;
# split the string up into its individual characters
@BASES = split(//, $line1);
# record the longest read length to determine how large the data
# matrix has grown later
if($#BASES > $maxLength) {
# $maxLength = $#BASES;
$maxLength = scalar @BASES; # Thanks Thomas Hack for the bug fix 02/09/2014 //weichun
}
# Set the which flag to false because the next odd line will be a score line
$whichLine--;
} else {
# read in the line
$line2 = $_;
# remove the new-line character
chomp $line2;
# split the line up into individual characters
@SCORES = split(//, $line2);
# Iterate over the posiions in the score line
foreach my $pos1 (0 .. $#SCORES) {
# Determine which base has been called and it to determine which column of the data
# matrix needs to be manipulated. The ascII value of the score line associated with
# this base minus 32 is then used to determine which row of the data matrix needs
# manipulation. Finally the count is increased for that position in the matrix.
if( $BASES[$pos1] eq 'A'){
$data[(ord($SCORES[$pos1])-$normal)][($pos1*$numBases)] += 1;
} elsif( $BASES[$pos1] eq 'T'){
$data[(ord($SCORES[$pos1])-$normal)][(($pos1*$numBases)+$Tpos)] += 1;
} elsif( $BASES[$pos1] eq 'G'){
$data[(ord($SCORES[$pos1])-$normal)][(($pos1*$numBases)+$Gpos)] += 1;
} elsif( $BASES[$pos1] eq 'C'){
$data[(ord($SCORES[$pos1])-$normal)][(($pos1*$numBases)+$Cpos)] += 1;
} else {
$data[(ord($SCORES[$pos1])-$normal)][(($pos1*$numBases)+$Npos)] += 1;
}
}
# the next odd line will be a called bases line so set the which flag back to true
$whichLine++;
}
}
# Increment the iterator
$iter++;
}
# Write the longest length of read to the output file.
print OUTFILE "Longest Length Read: $maxLength\n";
# Put column headings on the file tab delimited
foreach my $pos2 (0 .. ($maxLength - 1)) {
print OUTFILE "A$pos2\t";
}
foreach my $pos3(0 .. ($maxLength - 1)){
print OUTFILE "T$pos3\t";
}
foreach my $pos4(0 .. ($maxLength - 1)){
print OUTFILE "G$pos4\t";
}
foreach my $pos5(0 .. ($maxLength - 1)){
print OUTFILE "C$pos5\t";
}
foreach my $pos6(0 .. ($maxLength - 1)){
print OUTFILE "N$pos6\t";
}
print OUTFILE "\n";
# Re-arrange the elements of the matrix and calculate the average quality score per position.
for(my $h = 0; $h < $numBases; $h++){
for(my $t = 0; $t < $numScores; $t++) {
for(my $g = 0; $g < ($maxLength); $g++) {
# Set null elements to 0
if($data[$t][(($g*$numBases)+$h)] < 1){
$data[$t][(($g*$numBases)+$h)] = 0;
}
# Do the re-arranging
$finDat[$t][($g+(($maxLength)*$h))] = $data[$t][(($g*$numBases)+$h)];
# Do the summations needed to find avg quality scores
$avgScore[0][($g+(($maxLength)*$h))] += $allScores[$t]*$finDat[$t][($g+(($maxLength)*$h))];
$avgScore[1][($g+(($maxLength)*$h))] += $finDat[$t][($g+(($maxLength)*$h))];
}
}
}
# Write the data matrix to the output file tab delimited
for(my $o = 0; $o < ($numScores + 1); $o++) {
for(my $p = 0; $p < ($maxLength * $numBases); $p++) {
if($o == $numScores){
# Make sure the numerators and denominators are not 0.
if(($avgScore[0][$p] != 0) && ($avgScore[1][$p] != 0)){
print OUTFILE ($avgScore[0][$p] / $avgScore[1][$p]), "\t";
} else {
print OUTFILE "0\t";
}
} else {
print OUTFILE "$finDat[$o][$p]\t";
}
}
print OUTFILE "\n";
}
# Write the average quality score information to the file
for( my $n = 0; $n < 2; $n++){
for( my $m = 0; $m < ($maxLength *$numBases); $m++){
print OUTFILE $avgScore[$n][$m], "\t";
}
print OUTFILE "\n";
}
# Close the open files.
close(OUTFILE);
close(INFILE);
# Exit the program
exit;
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