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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=$3
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6
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7 dir="$(cd "$(dirname "$0")" && pwd)"
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8 mkdir $outputDir
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9
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10 Rscript --verbose $dir/RScript.r $inputFile $outputDir 2>&1
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11 cp $dir/jquery-1.11.0.min.js $outputDir
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12 cp $dir/script.js $outputDir
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13 cp $dir/style.css $outputDir
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14 cp $dir/tabber.js $outputDir
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15
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16 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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17
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18 cd $outputDir
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19
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20 html="index.html"
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21 echo "<html><head><title>Result</title>" > $html
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22 echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $html
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23 echo "<script type='text/javascript' src='tabber.js'></script>" >> $html
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24 echo "<script type='text/javascript' src='script.js'></script>" >> $html
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25 echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $html
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26 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $html
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27 echo "<div id='hidden_div' style='display: none;'></div>" >> $html
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28 echo "<div class='tabber'>" >> $html
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29 while read patient sample1 sample2
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30 do
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31 echo "$patient"
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32 oldLocus=""
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33 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
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34 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
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35 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
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36 echo "<div class='tabbertab' title='$patient'>" >> $html
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37 echo "<div class='tabber'>" >> $html
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38 echo "<div class='tabbertab' title='Data frequency'>" >> $html
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39 echo "<table><tr><td style='vertical-align:top;'>" >> $html
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40 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> $html
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2
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41 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>Normalized Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Normalized 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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42 echo "<tbody>" >> $html
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2
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43 readsumtable="<table class='result_table summary_table'><thead><tr><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Total normalized read count for $sample1</th><th>Total normalized read count for $sample2</th></tr></thead>"
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44 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
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0
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45 do
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46 if [ "$locus" != "$oldLocus" ] ; then
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47 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>" >> $html
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48 echo "<tr><td><b>$locus</b></td>" >> $html
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2
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49 readsumtable="${readsumtable}<tr><td>$locus</td><td>$v_segment</td><td>$j_segment</td><td>$locusreadsum1</td><td>$locusreadsum2</td></tr>"
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0
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50 else
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51 echo "<td></td>" >> $html
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52 fi
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53 echo "<td>$v_segment</td>" >> $html
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54 echo "<td>$j_segment</td>" >> $html
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55 echo "<td>>$cut_off_value</td>" >> $html
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56 if [ "$both" != "0" ] ; then
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57 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$both</td>" >> $html
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58 else
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59 echo "<td>$both</td>" >> $html
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60 fi
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61 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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62 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> $html
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63 else
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64 echo "<td>$one</td>" >> $html
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65 fi
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66 echo "<td>$read_count1</td>" >> $html
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67 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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68 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> $html
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69 else
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70 echo "<td>$two</td>" >> $html
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71 fi
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72 echo "<td>$read_count2</td>" >> $html
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73 echo "<td>$sum</td>" >> $html
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74 echo "<td>${percent}%</td>" >> $html
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75 echo "</tr>" >> $html
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2
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76 oldLocus="$locus"
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0
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77 done < tmp.txt
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78 echo "</tbody></table>" >> $html
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2
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79 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> $html
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80 echo "${readsumtable}</table></div>" >> $html
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0
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81 echo "<div class='tabbertab' title='Graphs frequency'>" >> $html
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82 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> $html
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83 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> $html
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84 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> $html
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85
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86 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
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87 echo "<div class='tabbertab' title='Data reads'>" >> $html
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88 echo "<table><tr><td style='vertical-align:top;'>" >> $html
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89 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> $html
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90 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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91 echo "<tbody>" >> $html
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2
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92 readsumtable="<table class='result_table summary_table'><thead><tr><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Total normalized read count for $sample1</th><th>Total normalized read count for $sample2</th></tr></thead>"
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93 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
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0
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94 do
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95 if [ "$locus" != "$oldLocus" ] ; then
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96 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>" >> $html
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97 echo "<tr><td><b>$locus</b></td>" >> $html
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2
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98 readsumtable="${readsumtable}<tr><td>$locus</td><td>$v_segment</td><td>$j_segment</td><td>$locusreadsum1</td><td>$locusreadsum2</td></tr>"
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0
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99 else
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100 echo "<td></td>" >> $html
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101 fi
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102 echo "<td>$v_segment</td>" >> $html
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103 echo "<td>$j_segment</td>" >> $html
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104 echo "<td>>$cut_off_value</td>" >> $html
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105 if [ "$both" != "0" ] ; then
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1
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106 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$both</td>" >> $html
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0
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107 else
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108 echo "<td>$both</td>" >> $html
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109 fi
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110 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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111 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> $html
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112 else
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113 echo "<td>$one</td>" >> $html
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114 fi
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115 echo "<td>$read_count1</td>" >> $html
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116 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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117 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> $html
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118 else
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119 echo "<td>$two</td>" >> $html
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120 fi
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121 echo "<td>$read_count2</td>" >> $html
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122 echo "<td>$sum</td>" >> $html
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123 echo "<td>${percent}%</td>" >> $html
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124 echo "</tr>" >> $html
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125 oldLocus="$locus"
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126 done < tmp.txt
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127 echo "</tbody></table>" >> $html
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2
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128 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> $html
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129 echo "${readsumtable}</table></div>" >> $html
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0
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130 echo "<div class='tabbertab' title='Graphs reads'>" >> $html
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131 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> $html
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132 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> $html
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133 echo "<a href='${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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134 echo "</div>" >> $html
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0
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135 echo "</div>" >> $html
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136 done < patients.txt
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137 echo "</div></html>" >> $html
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138 rm tmp.txt
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