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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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29
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8 merge_on="$6"
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0
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9
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10 dir="$(cd "$(dirname "$0")" && pwd)"
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11 mkdir $outputDir
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12
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3
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13
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29
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14 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells "${merge_on}" 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="${patient}.html"
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9
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33 echo "$header" > "$html"
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4
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34 if [[ "$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 ${patient}_freq.txt | sed "s/>//" > tmp.txt
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9
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49 echo "<div class='tabber'>" >> "$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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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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54 echo "<tbody>" >> "$html"
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30
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55 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>"
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2
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56 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
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0
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57 do
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58 if [ "$locus" != "$oldLocus" ] ; then
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9
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59 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
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60 echo "<tr><td><b>$locus</b></td>" >> "$html"
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0
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61 else
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9
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62 echo "<td></td>" >> "$html"
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0
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63 fi
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9
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64 echo "<td>$v_segment</td>" >> "$html"
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65 echo "<td>$j_segment</td>" >> "$html"
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66 echo "<td>>$cut_off_value</td>" >> "$html"
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67 if [ "$both" != "0" ] ; then
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68 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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0
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69 else
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70 echo "<td>$both</td>" >> "$html"
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0
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71 fi
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72 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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73 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html"
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0
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74 else
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75 echo "<td>$one</td>" >> "$html"
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0
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76 fi
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9
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77 echo "<td>$read_count1</td>" >> "$html"
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78 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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79 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html"
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0
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80 else
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9
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81 echo "<td>$two</td>" >> "$html"
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0
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82 fi
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9
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83 echo "<td>$read_count2</td>" >> "$html"
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84 echo "<td>$sum</td>" >> "$html"
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85 echo "<td>${percent}%</td>" >> "$html"
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86 echo "</tr>" >> "$html"
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29
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87 oldLocus="$locus"
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88 if [ "${cut_off_value}" == "0" ] ; then
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30
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89 scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /></td>"
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29
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90 fi
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0
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91 done < tmp.txt
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9
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92 echo "</tbody></table>" >> "$html"
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93 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
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94 echo "</div>" >> "$html"
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95 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
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96 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html"
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97 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html"
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98 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html"
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30
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99 echo "${scatterplot_tab}</tr></table></div>" >> "$html"
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0
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100
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101 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
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9
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102 echo "<div class='tabbertab' title='Data reads'>" >> "$html"
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103 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
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104 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
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105 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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106 echo "<tbody>" >> "$html"
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30
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107 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>"
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2
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108 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
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0
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109 do
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110 if [ "$locus" != "$oldLocus" ] ; then
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9
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111 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html"
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112 echo "<tr><td><b>$locus</b></td>" >> "$html"
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0
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113 else
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9
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114 echo "<td></td>" >> "$html"
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0
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115 fi
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9
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116 echo "<td>$v_segment</td>" >> "$html"
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117 echo "<td>$j_segment</td>" >> "$html"
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118 echo "<td>>$cut_off_value</td>" >> "$html"
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0
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119 if [ "$both" != "0" ] ; then
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120 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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121 else
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122 echo "<td>$both</td>" >> "$html"
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0
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123 fi
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124 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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125 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html"
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0
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126 else
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9
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127 echo "<td>$one</td>" >> "$html"
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0
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128 fi
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9
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129 echo "<td>$read_count1</td>" >> "$html"
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0
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130 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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131 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html"
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0
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132 else
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133 echo "<td>$two</td>" >> "$html"
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0
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134 fi
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135 echo "<td>$read_count2</td>" >> "$html"
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136 echo "<td>$sum</td>" >> "$html"
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137 echo "<td>${percent}%</td>" >> "$html"
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138 echo "</tr>" >> "$html"
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139 oldLocus="$locus"
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29
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140 if [ "${cut_off_value}" == "0" ] ; then
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30
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141 scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /></td>"
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29
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142 fi
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143 done < tmp.txt
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9
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144 echo "</tbody></table>" >> "$html"
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145 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"
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146 echo "</div>" >> "$html"
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147 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html"
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148 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> "$html"
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149 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> "$html"
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150 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html"
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30
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151 echo "${scatterplot_tab}</tr></table></div>" >> "$html"
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152 echo "</div>" >> "$html"
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153 echo "</div>" >> "$html"
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154 echo "</html>" >> "$html"
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155 done < patients.txt
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4
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156
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157 html="index.html"
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158 echo "<html>" > $html
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159 echo "<table>" >> "$html"
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29
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160 echo "<tr><td><b>Singles (<a href='singles_freq_scatterplot.png'>Frequency scatterplot</a>, <a href='singles_reads_scatterplot.png'>Reads scatterplot</a>):</b></td></tr>" >> "$html"
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4
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161 for patient in "${singles[@]}"
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162 do
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163 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
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4
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164 done
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9
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165 echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> "$html"
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4
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166 for patient in "${pairs_Left_Right[@]}"
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167 do
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9
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168 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
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4
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169 done
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170 echo "<tr><td><b>Pairs (BM & PB):</b></td></tr>" >> "$html"
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4
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171 for patient in "${pairs_BM_PB[@]}"
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172 do
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173 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
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4
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174 done
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9
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175 echo "<tr><td><b>Pairs (Dx & R):</b></td></tr>" >> "$html"
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4
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176 for patient in "${pairs_R_Dx[@]}"
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177 do
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178 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html"
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4
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179 done
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180 echo "<tr><td><b>Triplets:</b></td></tr>" >> "$html"
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4
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181
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7
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182 while read sample1 sample2 sample3
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183 do
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184 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')"
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185 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')"
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186 sample3="$(echo ${sample3} | tr -d '\r' | tr -d '\n')"
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187 patient="${sample1}_${sample2}_${sample3}"
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188 echo "$patient"
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189 html="${patient}.html"
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190 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html"
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191 echo "$header" > $html
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192 oldLocus=""
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193 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt
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9
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194 echo "<div class='tabber'>" >> "$html"
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195 echo "<div class='tabbertab' title='Data frequency'>" >> "$html"
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196 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
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197 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
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21
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198 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 ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
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9
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199 echo "<tbody>" >> "$html"
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23
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200 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'>"
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21
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201 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three
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7
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202 do
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203 if [ "$locus" != "$oldLocus" ] ; then
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9
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204 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>" >> "$html"
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205 echo "<tr><td><b>$locus</b></td>" >> "$html"
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7
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206 else
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9
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207 echo "<td></td>" >> "$html"
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7
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208 fi
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9
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209 echo "<td>$v_segment</td>" >> "$html"
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210 echo "<td>$j_segment</td>" >> "$html"
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211 echo "<td>>$cut_off_value</td>" >> "$html"
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7
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212 if [ "$all" != "0" ] ; then
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213 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$all</td>" >> "$html"
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7
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214 else
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9
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215 echo "<td>$all</td>" >> "$html"
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7
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216 fi
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217 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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9
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218 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html"
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7
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219 else
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9
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220 echo "<td>$one</td>" >> "$html"
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21
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221 fi
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7
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222 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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9
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223 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html"
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7
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224 else
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9
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225 echo "<td>$two</td>" >> "$html"
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7
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226 fi
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227 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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9
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228 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> "$html"
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7
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229 else
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9
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230 echo "<td>$three</td>" >> "$html"
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7
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231 fi
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21
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232
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233 if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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23
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234 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${one_two}</td>" >> "$html"
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21
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235 else
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236 echo "<td>${one_two}</td>" >> "$html"
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237 fi
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238 if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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23
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239 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${one_three}</td>" >> "$html"
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21
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240 else
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241 echo "<td>${one_three}</td>" >> "$html"
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242 fi
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243 if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
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23
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244 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${two_three}</td>" >> "$html"
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21
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245 else
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246 echo "<td>${two_three}</td>" >> "$html"
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247 fi
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248
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9
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249 echo "</tr>" >> "$html"
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23
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250 oldLocus="$locus"
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251 if [ "${cut_off_value}" == "0" ] ; then
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252 scatterplot_tab="${scatterplot_tab}<img src='${sample1}_${sample2}_${sample3}_freq_${locus}_scatter.png' /><br />"
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253 fi
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7
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254 done < tmp.txt
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9
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255 echo "</tbody></table>" >> "$html"
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256 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html"
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257 echo "</div>" >> "$html"
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258 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html"
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259 echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
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260 echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
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23
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261 echo "${scatterplot_tab}</div>" >> "$html"
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7
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262
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|
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263 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
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9
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264 echo "<div class='tabbertab' title='Data reads'>" >> "$html"
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265 echo "<table><tr><td style='vertical-align:top;'>" >> "$html"
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266 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
|
|
21
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267 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 ${patient}_All</th><th>Number of sequences_$sample1</th><th>Number of sequences_$sample2</th><th>Number of sequences_$sample3</th><th>Number of sequences_${sample1}_${sample2}</th><th>Number of sequences_${sample1}_${sample3}</th><th>Number of sequences_${sample2}_${sample3}</th></thead>" >> "$html"
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9
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268 echo "<tbody>" >> "$html"
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23
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269 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'>"
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21
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270 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three
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7
|
271 do
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|
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272 if [ "$locus" != "$oldLocus" ] ; then
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9
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273 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>" >> "$html"
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|
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274 echo "<tr><td><b>$locus</b></td>" >> "$html"
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7
|
275 else
|
|
9
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276 echo "<td></td>" >> "$html"
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|
7
|
277 fi
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|
9
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278 echo "<td>$v_segment</td>" >> "$html"
|
|
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279 echo "<td>$j_segment</td>" >> "$html"
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|
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280 echo "<td>>$cut_off_value</td>" >> "$html"
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|
7
|
281 if [ "$all" != "0" ] ; then
|
|
9
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282 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$all</td>" >> "$html"
|
|
7
|
283 else
|
|
9
|
284 echo "<td>$all</td>" >> "$html"
|
|
7
|
285 fi
|
|
|
286 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then
|
|
9
|
287 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html"
|
|
7
|
288 else
|
|
9
|
289 echo "<td>$one</td>" >> "$html"
|
|
7
|
290 fi
|
|
|
291 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then
|
|
9
|
292 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html"
|
|
7
|
293 else
|
|
9
|
294 echo "<td>$two</td>" >> "$html"
|
|
7
|
295 fi
|
|
|
296 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then
|
|
9
|
297 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> "$html"
|
|
7
|
298 else
|
|
9
|
299 echo "<td>$three</td>" >> "$html"
|
|
7
|
300 fi
|
|
21
|
301
|
|
|
302 if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
|
|
23
|
303 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${one_two}</td>" >> "$html"
|
|
21
|
304 else
|
|
|
305 echo "<td>${one_two}</td>" >> "$html"
|
|
|
306 fi
|
|
|
307 if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
|
|
23
|
308 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${one_three}</td>" >> "$html"
|
|
21
|
309 else
|
|
|
310 echo "<td>${one_three}</td>" >> "$html"
|
|
|
311 fi
|
|
|
312 if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then
|
|
23
|
313 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${two_three}</td>" >> "$html"
|
|
21
|
314 else
|
|
|
315 echo "<td>${two_three}</td>" >> "$html"
|
|
|
316 fi
|
|
|
317
|
|
9
|
318 echo "</tr>" >> "$html"
|
|
7
|
319 oldLocus="$locus"
|
|
23
|
320 if [ "${cut_off_value}" == "0" ] ; then
|
|
|
321 scatterplot_tab="${scatterplot_tab}<img src='${sample1}_${sample2}_${sample3}_reads_${locus}_scatter.png' /><br />"
|
|
|
322 fi
|
|
7
|
323 done < tmp.txt
|
|
9
|
324 echo "</tbody></table>" >> "$html"
|
|
|
325 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html"
|
|
|
326 echo "</div>" >> "$html"
|
|
|
327 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html"
|
|
|
328 echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> "$html"
|
|
|
329 echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html"
|
|
23
|
330 echo "${scatterplot_tab}</div>" >> "$html"
|
|
9
|
331 echo "</div>" >> "$html"
|
|
|
332 echo "</div>" >> "$html"
|
|
|
333 echo "</html>" >> "$html"
|
|
7
|
334 done < triplets.txt
|
|
|
335 rm tmp.txt
|
|
|
336
|
|
|
337
|
|
|
338 html="index.html"
|
|
|
339
|
|
9
|
340 echo "</table>" >> "$html"
|
|
|
341 echo "</html>" >> "$html"
|
|
4
|
342
|
|
23
|
343
|
