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0
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1 #!/bin/bash
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2
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3 inputFile=$1
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4 outputFile=$2
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5 outputDir=$3
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3
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6 min_freq=$4
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7 min_cells=$5
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0
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8
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9 dir="$(cd "$(dirname "$0")" && pwd)"
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10 mkdir $outputDir
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11
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3
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12 echo "testtestsetset" > $outputFile
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13
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14 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells 2>&1
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0
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15 cp $dir/jquery-1.11.0.min.js $outputDir
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16 cp $dir/script.js $outputDir
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17 cp $dir/style.css $outputDir
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18 cp $dir/tabber.js $outputDir
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19
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20 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)</center></html>" > $outputFile
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21
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22 cd $outputDir
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23
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4
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24 header="<html><head><script type='text/javascript' src='jquery-1.11.0.min.js'></script><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'></head><div id='hidden_div' style='display: none;'></div>"
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25 singles=()
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26 pairs_BM_PB=()
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27 pairs_Left_Right=()
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28 pairs_R_Dx=()
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29 while read patient sample1 sample2 type
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0
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30 do
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31 echo "$patient"
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4
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32 html="${patient}.html"
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33 echo "$header" > $html
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34 if [[ "$type" == *pair* ]] ; then
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35 if [[ "$sample1" == *_BM* ]] || [[ "$sample1" == *_PB* ]] ; then
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36 pairs_BM_PB+=( "$patient" )
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37 elif [[ "$sample1" == *_Left* ]] || [[ "$sample1" == *_Right* ]] ; then
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38 pairs_Left_Right+=( "$patient" )
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39 else
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40 pairs_R_Dx+=( "$patient" )
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41 fi
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42 else
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43 singles+=( "$patient" )
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44 fi
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0
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45 oldLocus=""
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46 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
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47 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
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48 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
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49 echo "<div class='tabber'>" >> $html
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50 echo "<div class='tabbertab' title='Data frequency'>" >> $html
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51 echo "<table><tr><td style='vertical-align:top;'>" >> $html
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52 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html
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4
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53 echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html
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0
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54 echo "<tbody>" >> $html
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2
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55 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
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0
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56 do
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57 if [ "$locus" != "$oldLocus" ] ; then
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58 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
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59 echo "<tr><td><b>$locus</b></td>" >> $html
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60 else
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61 echo "<td></td>" >> $html
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62 fi
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63 echo "<td>$v_segment</td>" >> $html
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64 echo "<td>$j_segment</td>" >> $html
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65 echo "<td>>$cut_off_value</td>" >> $html
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66 if [ "$both" != "0" ] ; then
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67 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$both</td>" >> $html
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68 else
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69 echo "<td>$both</td>" >> $html
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70 fi
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71 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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72 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> $html
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73 else
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74 echo "<td>$one</td>" >> $html
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75 fi
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76 echo "<td>$read_count1</td>" >> $html
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77 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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78 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> $html
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79 else
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80 echo "<td>$two</td>" >> $html
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81 fi
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82 echo "<td>$read_count2</td>" >> $html
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83 echo "<td>$sum</td>" >> $html
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84 echo "<td>${percent}%</td>" >> $html
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85 echo "</tr>" >> $html
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2
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86 oldLocus="$locus"
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0
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87 done < tmp.txt
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88 echo "</tbody></table>" >> $html
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2
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89 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html
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90 echo "</div>" >> $html
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91 echo "<div class='tabbertab' title='Graphs frequency'>" >> $html
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92 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> $html
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93 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> $html
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94 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> $html
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95
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96 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
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97 echo "<div class='tabbertab' title='Data reads'>" >> $html
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98 echo "<table><tr><td style='vertical-align:top;'>" >> $html
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99 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html
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100 echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> $html
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101 echo "<tbody>" >> $html
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2
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102 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
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0
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103 do
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104 if [ "$locus" != "$oldLocus" ] ; then
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105 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> $html
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106 echo "<tr><td><b>$locus</b></td>" >> $html
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107 else
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108 echo "<td></td>" >> $html
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109 fi
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110 echo "<td>$v_segment</td>" >> $html
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111 echo "<td>$j_segment</td>" >> $html
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112 echo "<td>>$cut_off_value</td>" >> $html
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113 if [ "$both" != "0" ] ; then
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1
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114 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$both</td>" >> $html
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0
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115 else
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116 echo "<td>$both</td>" >> $html
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117 fi
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118 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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119 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> $html
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120 else
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121 echo "<td>$one</td>" >> $html
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122 fi
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123 echo "<td>$read_count1</td>" >> $html
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124 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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125 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> $html
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126 else
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127 echo "<td>$two</td>" >> $html
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128 fi
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129 echo "<td>$read_count2</td>" >> $html
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130 echo "<td>$sum</td>" >> $html
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131 echo "<td>${percent}%</td>" >> $html
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132 echo "</tr>" >> $html
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133 oldLocus="$locus"
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134 done < tmp.txt
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135 echo "</tbody></table>" >> $html
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136 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html
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4
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137 echo "</div>" >> $html
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138 echo "<div class='tabbertab' title='Graphs reads'>" >> $html
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139 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
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140 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> $html
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141 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> $html
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2
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142 echo "</div>" >> $html
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143 echo "</div>" >> $html
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144 echo "</html>" >> $html
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145 done < patients.txt
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146 rm tmp.txt
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4
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147
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148 html="index.html"
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149 echo "<html>" > $html
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150 echo "<table>" >> $html
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151 echo "<tr><td><b>Singles:</b></td></tr>" >> $html
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152 for patient in "${singles[@]}"
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153 do
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154 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
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155 done
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156 echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> $html
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157 for patient in "${pairs_Left_Right[@]}"
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158 do
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159 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
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160 done
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161 echo "<tr><td><b>Pairs (BM & PB):</b></td></tr>" >> $html
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162 for patient in "${pairs_BM_PB[@]}"
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163 do
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164 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
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165 done
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166 echo "<tr><td><b>Pairs (Dx & R):</b></td></tr>" >> $html
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167 for patient in "${pairs_R_Dx[@]}"
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168 do
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169 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> $html
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170 done
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171 echo "<tr><td><b>Triplets:</b></td></tr>" >> $html
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172
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173 echo "</table>" >> $html
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174 echo "</html>" >> $html
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175
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