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5
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1 #!/bin/bash
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2
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3 inputFile=$1
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4 outputDir=$3
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5 outputFile=$3/index.html #$2
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6 clonalType=$4
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7 species=$5
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8 locus=$6
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9 filterproductive=$7
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10 clonality_method=$8
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11
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12 dir="$(cd "$(dirname "$0")" && pwd)"
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13 useD="false"
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14 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
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15 echo "species D region in reference db"
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16 useD="true"
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17 fi
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18 echo "$species"
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19 if [[ "$species" == *"custom"* ]] ; then
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20 loci=(${locus//;/ })
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21 useD="true"
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22 echo "${loci[@]}"
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23 if [[ "${#loci[@]}" -eq "2" ]] ; then
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24 useD="false"
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25 fi
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26 fi
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27 mkdir $3
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28 cp $dir/genes.txt $outputDir
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29 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1
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30 cp $dir/tabber.js $outputDir
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31 cp $dir/style.css $outputDir
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32 cp $dir/script.js $outputDir
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33 cp $dir/jquery-1.11.0.min.js $outputDir
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34 cp $dir/pure-min.css $outputDir
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35 samples=`cat $outputDir/samples.txt`
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36
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37 echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)<br />" > $2
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38 echo "<table border = 1>" >> $2
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39 echo "<thead><tr><th>Sample/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
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40 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un
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41 do
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42 echo "<tr><td>$sample</td>" >> $2
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43 echo "<td>$all</td>" >> $2
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44 echo "<td>$productive (${perc_prod}%)</td>" >> $2
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45 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2
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46 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2
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47 echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2
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48 done < $outputDir/productive_counting.txt
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49 echo "</table border></center></html>" >> $2
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50
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51 echo "<html><head><title>Report on:" >> $outputFile
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52
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53 mkdir $outputDir/circos
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54 cp $dir/circos/* $outputDir/circos/
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55 #CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
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56 #CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
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57
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58 #CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
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59 #CIRCOSDIR="/home/galaxy/Anaconda3/bin"
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60
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61 USECIRCOS="no"
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62 if [ -d "$CIRCOSDIR" ]; then
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63 USECIRCOS="yes"
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64 else
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12
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65 if [ -d "/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" ]; then #hopefully temporary fix
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5
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66 USECIRCOS="yes"
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67 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
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68 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
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69 fi
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12
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70
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71 if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix
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72 USECIRCOS="yes"
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73 CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
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74 CIRCOSDIR="/home/galaxy/Anaconda3/bin"
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75 fi
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5
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76 fi
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12
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77
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5
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78 echo "Using Circos: $USECIRCOS"
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79 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
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80 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
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81 echo " $sample" >> $outputFile
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82
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83 if [[ "$USECIRCOS" != "yes" ]]; then
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84 continue
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85 fi
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86
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87 circos_file="$outputDir/${sample}_VJ_circos.txt"
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88 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
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89 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
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90 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
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91 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
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92
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93
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94 if [[ "$useD" == "true" ]] ; then
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95 circos_file="$outputDir/${sample}_VD_circos.txt"
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96 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
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97 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
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98 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
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99 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
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100
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101 circos_file="$outputDir/${sample}_DJ_circos.txt"
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102 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
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103 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
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104 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
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105 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
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106
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107 fi
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108 done
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109 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
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110 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $outputFile
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111 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
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112 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
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113 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
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114 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
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115
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8
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116
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5
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117 echo "<img src='VFPlot.png'/>" >> $outputFile
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118 if [[ "$useD" == "true" ]] ; then
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119 echo "<img src='DFPlot.png'/>" >> $outputFile
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120 fi
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121 echo "<img src='VPlot.png'/>" >> $outputFile
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122 if [[ "$useD" == "true" ]] ; then
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123 echo "<img src='DPlot.png'/>" >> $outputFile
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124 fi
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125 echo "<img src='JPlot.png'/>" >> $outputFile
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8
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126 echo "</div>" >> $outputFile
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127
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128 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile
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129 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
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5
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130 echo "<img src='AAComposition.png'/>" >> $outputFile
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131 echo "<img src='DReadingFrame.png'/>" >> $outputFile
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8
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132
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133 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
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134 echo "<thead><tr><th>Sample</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
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135 while IFS=, read Sample median
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136 do
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137 echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile
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138 done < $outputDir/AAMedianBySample.csv
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139 echo "</table>" >> $outputFile
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140
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5
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141 echo "</div>" >> $outputFile
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142
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143 #Heatmaps
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144
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145 count=1
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146 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
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147 for sample in $samples; do
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148 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
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149 if [[ "$useD" == "true" ]] ; then
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150 echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile
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151 fi
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152 echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile
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153 if [[ "$useD" == "true" ]] ; then
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154 echo "<td><img src='HeatmapDJ_$sample.png'/></td>" >> $outputFile
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155 fi
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156 echo "</tr></table></div>" >> $outputFile
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157 count=$((count+1))
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158 done
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159 echo "</div></div>" >> $outputFile
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160
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161 #circos
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162
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163 if [[ "$USECIRCOS" == "yes" ]]; then
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164
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165 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
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166 for sample in $samples; do
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167 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile
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168 if [[ "$useD" == "true" ]] ; then
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169 echo "<tr><td>V-D</td><td><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
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170 fi
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171 echo "<tr><td>V-J</td><td><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
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172 if [[ "$useD" == "true" ]] ; then
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173 echo "<tr><td>D-J</td><td><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
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174 fi
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175 echo "<center></table></div>" >> $outputFile
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176 count=$((count+1))
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177 done
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178 echo "</div></div>" >> $outputFile
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179 fi
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180 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
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181
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182 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
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183 echo "$hasReplicateColumn"
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184 #if its a 'new' merged file with replicate info
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185 if [[ "$hasReplicateColumn" == "Yes" ]] ; then
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186 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
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187 for sample in $samples; do
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188 echo "${clonality_method}"
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189 if [[ "${clonality_method}" == "old" ]] ; then
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190 echo "in old"
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191 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
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192 echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
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193 echo "<thead><tr><th colspan='4'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile
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194
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195 #replicate,reads,squared
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16
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196 echo "<tr><td>Replicate ID</td><td>Number of Reads</td></tr>" >> $outputFile
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5
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197 while IFS=, read replicate reads squared
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198 do
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16
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199 echo "<tr><td>$replicate</td><td>$reads</td></tr>" >> $outputFile
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5
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200 done < $outputDir/ReplicateReads_$sample.csv
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201
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202 #sum of reads and reads squared
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203 while IFS=, read readsSum squaredSum
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204 do
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16
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205 echo "<tr><td>Sum</td><td>$readsSum</td></tr>" >> $outputFile
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5
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206 done < $outputDir/ReplicateSumReads_$sample.csv
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207
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208 #overview
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16
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209 echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td></tr>" >> $outputFile
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5
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210 while IFS=, read type count weight weightedCount
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211 do
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212 if [[ "$type" -eq "1" ]]; then
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16
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213 echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
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5
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214 else
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16
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215 echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td></tr>" >> $outputFile
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5
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216 fi
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217
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218 done < $outputDir/ClonalityOverView_$sample.csv
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219 echo "</table></div>" >> $outputFile
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220 else
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221 echo "in new"
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222 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.csv)"
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223 echo "<div class='tabbertab' title='$sample'>" >> $outputFile
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224 echo "Lymphclon clonality score: <br />$clonalityScore<br /><br />" >> $outputFile
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225 echo "<table border = 1>" >> $outputFile
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226 while IFS=, read type count
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227 do
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228 echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
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229 done < $outputDir/lymphclon_coincidences_$sample.csv
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230 echo "</table></div>" >> $outputFile
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231 fi
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232 done
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233 echo "</div></div>" >> $outputFile
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234 fi
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235
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236 #hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
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237
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238 #if [[ "$hasJunctionData" == "Yes" ]] ; then
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239 if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then
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240 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
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241 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
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242 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
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243 do
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244 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
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245 done < $outputDir/junctionAnalysisProd_mean.csv
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246 echo "</tbody></table>" >> $outputFile
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247
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248 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
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249 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
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250 do
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251 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
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252 done < $outputDir/junctionAnalysisUnProd_mean.csv
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253 echo "</tbody></table>" >> $outputFile
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254
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255 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
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256 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
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257 do
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258 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
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259 done < $outputDir/junctionAnalysisProd_median.csv
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260 echo "</tbody></table>" >> $outputFile
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261
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262 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
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263 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
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264 do
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265 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
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266 done < $outputDir/junctionAnalysisUnProd_median.csv
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267 echo "</tbody></table>" >> $outputFile
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268
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269 echo "</div>" >> $outputFile
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270 fi
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271
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272 echo "<div class='tabbertab' title='Comparison'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>" >> $outputFile
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273 for sample in $samples; do
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274 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
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275 done
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276 echo "</table><div name='comparisonarea'>" >> $outputFile
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277 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
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278 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
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279 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
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280 echo "</div></div>" >> $outputFile
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281
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282 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
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283 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
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284 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
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285 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>Download</a></td></tr>" >> $outputFile
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286 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile
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287
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288 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
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289
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290 echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile
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291 if [[ "$useD" == "true" ]] ; then
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292 echo "<tr><td>The dataset used to generate the D gene family frequency graph</td><td><a href='DFFrequency.csv'>Download</a></td></tr>" >> $outputFile
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293 fi
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294
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295 echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile
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296 if [[ "$useD" == "true" ]] ; then
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297 echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile
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298 fi
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299 echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile
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300 echo "<tr><td>The dataset used to generate the AA composition graph</td><td><a href='AAComposition.csv'>Download</a></td></tr>" >> $outputFile
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301
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302 for sample in $samples; do
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303 if [[ "$useD" == "true" ]] ; then
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304 echo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href='HeatmapVD_$sample.csv'>Download</a></td></tr>" >> $outputFile
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305 fi
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306 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
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307 if [[ "$useD" == "true" ]] ; then
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308 echo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href='HeatmapDJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
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309 fi
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310 done
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311
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312 echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile
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313
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314 echo "</table>" >> $outputFile
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315 echo "</div></html>" >> $outputFile
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