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53
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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 cp $dir/IGH_junctie_analyse.png $outputDir
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36 samples=`cat $outputDir/samples.txt`
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37
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38 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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39 echo "<table border = 1>" >> $2
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40 echo "<thead><tr><th>Donor/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
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41 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un
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42 do
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43 echo "<tr><td>$sample</td>" >> $2
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44 echo "<td>$all</td>" >> $2
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45 if [[ "$productive" != "0" ]] ; then
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46 echo "<td>$productive (${perc_prod}%)</td>" >> $2
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47 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2
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48 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2
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49 echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2
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50 else
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51 echo "<td colspan='4' style='background-color: red;'>No productive sequences!</td>" >> $2
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52 fi
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53 done < $outputDir/productive_counting.txt
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54 echo "</table><br />" >> $2
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55 echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate. <br />" >> $2
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56 echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2
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57 echo "</center></html>" >> $2
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58
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59 echo "<html><head><title>Report on:" >> $outputFile
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60
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61 mkdir $outputDir/circos
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62 cp -R $dir/circos/* $outputDir/circos/
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63
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64 USECIRCOS="no"
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65 path_to_circos=$(which circos)
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66 if [ -x "$path_to_circos" ]; then
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67 USECIRCOS="yes"
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68 fi
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69
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70 echo "Using Circos: $USECIRCOS"
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71 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
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72 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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73 echo " $sample" >> $outputFile
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74
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75 if [[ "$USECIRCOS" != "yes" ]]; then
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76 continue
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77 fi
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78
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79 circos_file="$outputDir/${sample}_VJ_circos.txt"
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80 sed -i -- 's%/%:%g' $circos_file
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81 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
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82 echo "Circos tools command:"
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83 echo "cat \"${circos_file}\" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/"
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84 cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
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85
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86 echo "Circos command:"
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87 echo "circos -conf $outputDir/circos/circos.conf 2>&1"
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88 circos -conf $outputDir/circos/circos.conf 2>&1
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89 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
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90 mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg
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91
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92
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93 if [[ "$useD" == "true" ]] ; then
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94 circos_file="$outputDir/${sample}_VD_circos.txt"
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95 sed -i -- 's%/%:%g' $circos_file
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96 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
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97 cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
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98 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
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99 circos -conf $outputDir/circos/circos.conf 2>&1
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100 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
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101 mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg
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102
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103 circos_file="$outputDir/${sample}_DJ_circos.txt"
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104 sed -i -- 's%/%:%g' $circos_file
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105 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
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106 cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/
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107 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt
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108 circos -conf $outputDir/circos/circos.conf 2>&1
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109 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
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110 mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg
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111 fi
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112 done
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113 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
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114 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $outputFile
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115 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
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116 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
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117 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
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118 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
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119
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120
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121 echo "<a href='VFPlot.pdf'><img src='VFPlot.png'/></a>" >> $outputFile
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122 if [[ "$useD" == "true" ]] ; then
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123 echo "<a href='DFPlot.pdf'><img src='DFPlot.png'/></a>" >> $outputFile
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124 fi
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125 echo "<a href='VPlot.pdf'><img src='VPlot.png'/></a>" >> $outputFile
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126 if [[ "$useD" == "true" ]] ; then
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127 echo "<a href='DPlot.pdf'><img src='DPlot.png'/></a>" >> $outputFile
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128 fi
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129 echo "<a href='JPlot.pdf'><img src='JPlot.png'/></a> <br />" >> $outputFile
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130
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131 echo "<a href='DReadingFrame.pdf'><img src='DReadingFrame.png'/></a>" >> $outputFile
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132
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133 cat $dir/naive_gene_freq.htm >> $outputFile
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134
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135 echo "</div>" >> $outputFile
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136
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137 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile
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138 echo "<a href='CDR3LengthPlot.pdf'><img src='CDR3LengthPlot.png'/></a><br />" >> $outputFile
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139 echo "<a href='AAComposition.pdf'><img src='AAComposition.png'/></a>" >> $outputFile
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140
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141
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142 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
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143 echo "<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
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144 while read Sample median
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145 do
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146 echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile
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147 done < $outputDir/AAMedianBySample.txt
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148 echo "</table>" >> $outputFile
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149
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150 cat $dir/naive_cdr3_char.htm >> $outputFile
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151
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152 echo "</div>" >> $outputFile
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153
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154 #Heatmaps
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155
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156 count=1
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157 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
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158 for sample in $samples; do
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159 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
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160 if [[ "$useD" == "true" ]] ; then
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161 echo "<td><a href='HeatmapVD_$sample.pdf'><img src='HeatmapVD_$sample.png'/></a></td>" >> $outputFile
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162 fi
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163 echo "<td><a href='HeatmapVJ_$sample.pdf'><img src='HeatmapVJ_$sample.png'/></a></td>" >> $outputFile
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164 if [[ "$useD" == "true" ]] ; then
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165 echo "<td><a href='HeatmapDJ_$sample.pdf'><img src='HeatmapDJ_$sample.png'/></a></td>" >> $outputFile
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166 fi
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167 echo "</tr></table></div>" >> $outputFile
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168 count=$((count+1))
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169 done
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170
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171 cat $dir/naive_heatmap.htm >> $outputFile
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172
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173 echo "</div></div>" >> $outputFile
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174
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175 echo "<div class='tabbertab' title='Compare Heatmaps'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>" >> $outputFile
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176 for sample in $samples; do
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177 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
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178 done
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179 echo "</table><div name='comparisonarea'>" >> $outputFile
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180 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
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181 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
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182 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
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183
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184 cat $dir/naive_compare.htm >> $outputFile
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185
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186 echo "</div></div>" >> $outputFile
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187
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188
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189 #circos
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190
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191 if [[ "$USECIRCOS" == "yes" ]]; then
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192
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193 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
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194 for sample in $samples; do
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195 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile
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196 if [[ "$useD" == "true" ]] ; then
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197 echo "<tr><td>V-D</td><td><a href='circosVD_${sample}.svg'><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
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198 fi
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199 echo "<tr><td>V-J</td><td><a href='circosVJ_${sample}.svg'><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
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200 if [[ "$useD" == "true" ]] ; then
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201 echo "<tr><td>D-J</td><td><a href='circosDJ_${sample}.svg'><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
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202 fi
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203 echo "<center></table></div>" >> $outputFile
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204 count=$((count+1))
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205 done
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206
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207 cat $dir/naive_circos.htm >> $outputFile
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208
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209 echo "</div></div>" >> $outputFile
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210 fi
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211 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
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212
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213 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
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214 echo "$hasReplicateColumn"
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215 #if its a 'new' merged file with replicate info
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216 if [[ "$hasReplicateColumn" == "Yes" && "${clonality_method}" != "none" ]] ; then
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217 if [[ "${clonality_method}" == "boyd" ]] ; then
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218 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
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219 else
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220 echo "<div class='tabbertab' title='Shared Clonal Types'><div class='tabber'>" >> $outputFile
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221 fi
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222
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223 for sample in $samples; do
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224 echo "${clonality_method}"
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225
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226 echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
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227
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228 if [[ "${clonality_method}" == "boyd" ]] ; then
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229 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.txt)"
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230 echo "<tr><td>Clonality Score: </td><td>$clonalityScore</td></tr>" >> $outputFile
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231 fi
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232
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233 #replicate,reads,squared
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234 echo "<tr><td>Replicate ID</td><td>Number of Sequences</td></tr>" >> $outputFile
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235 while read replicate reads squared
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236 do
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237 echo "<tr><td>$replicate</td><td>$reads</td></tr>" >> $outputFile
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238 done < $outputDir/ReplicateReads_$sample.txt
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239
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240 #sum of reads and reads squared
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241 while read readsSum squaredSum
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242 do
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243 echo "<tr><td>Sum</td><td>$readsSum</td></tr>" >> $outputFile
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244 done < $outputDir/ReplicateSumReads_$sample.txt
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245
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246 echo "<tr><td></td><td></td></tr>" >> $outputFile
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247
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248 #overview
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249 echo "<tr><td>Number of replicates containing the coincidence</td><td>Number of sequences shared between replicates</td></tr>" >> $outputFile
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250 while read type count weight weightedCount
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251 do
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252 if [[ "$type" -eq "1" ]]; then
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253 echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
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254 else
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255 echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td></tr>" >> $outputFile
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256 fi
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257 done < $outputDir/ClonalityOverView_$sample.txt
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258 echo "</table></div>" >> $outputFile
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259 done
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260
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261 cat $dir/naive_clonality.htm >> $outputFile
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262
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263 echo "</div></div>" >> $outputFile
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264 fi
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265
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266 #hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
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267
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268 #if [[ "$hasJunctionData" == "Yes" ]] ; then
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269 if [ -a "$outputDir/junctionAnalysisProd_mean_wD.txt" ] ; then
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270 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
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271 echo "<img src='IGH_junctie_analyse.png' />" >> $outputFile
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272
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273 echo "<center><p style='font-size: 20;'>Unique rearrangements with a V, D and J gene assigned</p></center>" >> $outputFile
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274 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</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>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
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275 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
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276 do
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277 echo "<tr><td>$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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278 done < $outputDir/junctionAnalysisProd_mean_wD.txt
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279 echo "</tbody></table>" >> $outputFile
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280
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281 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</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>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
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282 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
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283 do
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284 echo "<tr><td>$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>-</td></tr>" >> $outputFile
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285 done < $outputDir/junctionAnalysisUnProd_mean_wD.txt
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286 echo "</tbody></table>" >> $outputFile
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287
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288 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Donor</th><th>Number of sequences</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>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
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289 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
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290 do
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291 echo "<tr><td>$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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292 done < $outputDir/junctionAnalysisProd_median_wD.txt
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293 echo "</tbody></table>" >> $outputFile
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294
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295 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</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>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
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296 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
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297 do
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298 echo "<tr><td>$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>-</td></tr>" >> $outputFile
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299 done < $outputDir/junctionAnalysisUnProd_median_wD.txt
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300 echo "</tbody></table>" >> $outputFile
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301
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302 # again for no-d
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303 echo "<center><p style='font-size: 20;'>Unique rearrangements with only a V and J gene assigned</p></center>" >> $outputFile
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304 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
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305 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
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306 do
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307 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
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308 done < $outputDir/junctionAnalysisProd_mean_nD.txt
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309 echo "</tbody></table>" >> $outputFile
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310
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311 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
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312 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
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313 do
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314 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
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315 done < $outputDir/junctionAnalysisUnProd_mean_nD.txt
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316 echo "</tbody></table>" >> $outputFile
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317
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318 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
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319 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
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320 do
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321 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
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322 done < $outputDir/junctionAnalysisProd_median_nD.txt
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323 echo "</tbody></table>" >> $outputFile
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324
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325 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
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326 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
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327 do
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328 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
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329 done < $outputDir/junctionAnalysisUnProd_median_nD.txt
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330 echo "</tbody></table>" >> $outputFile
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331
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332 cat $dir/naive_junction.htm >> $outputFile
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333
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334 echo "</div>" >> $outputFile
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335 fi
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336
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337 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
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338 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
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339 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
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340 echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile
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341 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>" >> $outputFile
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342
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343 echo "<tr><td>The dataset used to generate the distribution of V gene families graph</td><td><a href='VFFrequency.txt'>Download</a></td></tr>" >> $outputFile
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344 if [[ "$useD" == "true" ]] ; then
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345 echo "<tr><td>The dataset used to generate the distribution of D gene families graph</td><td><a href='DFFrequency.txt'>Download</a></td></tr>" >> $outputFile
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346 fi
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347
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348 echo "<tr><td>The dataset used to generate the relative frequency of V gene usage graph</td><td><a href='VFrequency.txt'>Download</a></td></tr>" >> $outputFile
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349 if [[ "$useD" == "true" ]] ; then
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350 echo "<tr><td>The dataset used to generate the relative frequency of D gene usage graph</td><td><a href='DFrequency.txt'>Download</a></td></tr>" >> $outputFile
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351 fi
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352 echo "<tr><td>The dataset used to generate the relative frequency of J gene usage graph</td><td><a href='JFrequency.txt'>Download</a></td></tr>" >> $outputFile
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353 echo "<tr><td>The dataset used to generate the relative frequency of the D reading frame graph</td><td><a href='DReadingFrame.txt'>Download</a></td></tr>" >> $outputFile
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354
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355 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CDR3 Characteristics</td></tr>" >> $outputFile
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356 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.txt'>Download</a></td></tr>" >> $outputFile
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357 echo "<tr><td>The dataset used to generate the Amino Acid Composition in the CDR3 graph</td><td><a href='AAComposition.txt'>Download</a></td></tr>" >> $outputFile
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358
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359 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Heatmaps</td></tr>" >> $outputFile
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360 for sample in $samples; do
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361 if [[ "$useD" == "true" ]] ; then
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362 echo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href='HeatmapVD_$sample.txt'>Download</a></td></tr>" >> $outputFile
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363 fi
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364 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.txt'>Download</a></td></tr>" >> $outputFile
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365 if [[ "$useD" == "true" ]] ; then
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366 echo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href='HeatmapDJ_$sample.txt'>Download</a></td></tr>" >> $outputFile
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367 fi
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368 done
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369
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370 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Circos</td></tr>" >> $outputFile
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371 for sample in $samples; do
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372 if [[ "$useD" == "true" ]] ; then
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373 echo "<tr><td>The data used to generate the VD Circos plots for $sample.</td><td><a href='${sample}_VD_circos.txt'>Download</a></td></tr>" >> $outputFile
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374 fi
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375 echo "<tr><td>The data used to generate the VJ Circos plots for $sample.</td><td><a href='${sample}_VJ_circos.txt'>Download</a></td></tr>" >> $outputFile
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376 if [[ "$useD" == "true" ]] ; then
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377 echo "<tr><td>The data used to generate the DJ Circos plots for $sample.</td><td><a href='${sample}_DJ_circos.txt'>Download</a></td></tr>" >> $outputFile
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378 fi
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379 done
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380
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381 #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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382
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383 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $outputFile
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384 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.txt'>Download</a></td></tr>" >> $outputFile
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385 # echo "<tr><td>Sequences that are present in more than one replicate</td><td><a href='clonaltypes_replicates.txt'>Download</a></td></tr>" >> $outputFile
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386
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387 echo "</table>" >> $outputFile
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388
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389 cat $dir/naive_downloads.htm >> $outputFile
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390
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391 echo "</div></html>" >> $outputFile
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