Mercurial > repos > davidvanzessen > prisca
comparison wrapper.sh @ 0:ed6885c85660 draft
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| author | davidvanzessen |
|---|---|
| date | Wed, 31 Aug 2016 05:31:47 -0400 |
| parents | |
| children | 75853bceec00 |
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| -1:000000000000 | 0:ed6885c85660 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 inputFile=$1 | |
| 4 outputFile=$2 | |
| 5 outputDir=$3 | |
| 6 min_freq=$4 | |
| 7 min_cells=$5 | |
| 8 merge_on="$6" | |
| 9 | |
| 10 dir="$(cd "$(dirname "$0")" && pwd)" | |
| 11 mkdir $outputDir | |
| 12 | |
| 13 | |
| 14 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputFile $min_freq $min_cells "${merge_on}" 2>&1 | |
| 15 cp $dir/jquery-1.11.0.min.js $outputDir | |
| 16 cp $dir/script.js $outputDir | |
| 17 cp $dir/style.css $outputDir | |
| 18 cp $dir/tabber.js $outputDir | |
| 19 mv "$outputFile" "$outputDir/log.html" | |
| 20 | |
| 21 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 | |
| 22 | |
| 23 cd $outputDir | |
| 24 | |
| 25 header="<html><head><script type='text/javascript' src='jquery-1.11.0.min.js'></script><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'></head><div id='hidden_div' style='display: none;'></div>" | |
| 26 singles=() | |
| 27 pairs_BM_PB=() | |
| 28 pairs_Left_Right=() | |
| 29 pairs_R_Dx=() | |
| 30 while read patient sample1 sample2 type | |
| 31 do | |
| 32 echo "$patient" | |
| 33 html="${patient}.html" | |
| 34 echo "$header" > "$html" | |
| 35 if [[ "$type" == *pair* ]] ; then | |
| 36 if [[ "$sample1" == *_BM* ]] || [[ "$sample1" == *_PB* ]] ; then | |
| 37 pairs_BM_PB+=( "$patient" ) | |
| 38 elif [[ "$sample1" == *_Left* ]] || [[ "$sample1" == *_Right* ]] ; then | |
| 39 pairs_Left_Right+=( "$patient" ) | |
| 40 else | |
| 41 pairs_R_Dx+=( "$patient" ) | |
| 42 fi | |
| 43 else | |
| 44 singles+=( "$patient" ) | |
| 45 fi | |
| 46 oldLocus="" | |
| 47 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')" | |
| 48 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')" | |
| 49 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt | |
| 50 echo "<div class='tabber'>" >> "$html" | |
| 51 echo "<div class='tabbertab' title='Data frequency'>" >> "$html" | |
| 52 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" | |
| 53 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html" | |
| 54 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" | |
| 55 echo "<tbody>" >> "$html" | |
| 56 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>" | |
| 57 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 | |
| 58 do | |
| 59 if [ "$locus" != "$oldLocus" ] ; then | |
| 60 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" | |
| 61 echo "<tr><td><b>$locus</b></td>" >> "$html" | |
| 62 else | |
| 63 echo "<td></td>" >> "$html" | |
| 64 fi | |
| 65 echo "<td>$v_segment</td>" >> "$html" | |
| 66 echo "<td>$j_segment</td>" >> "$html" | |
| 67 echo "<td>>$cut_off_value</td>" >> "$html" | |
| 68 if [ "$both" != "0" ] ; then | |
| 69 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$both</td>" >> "$html" | |
| 70 else | |
| 71 echo "<td>$both</td>" >> "$html" | |
| 72 fi | |
| 73 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 74 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html" | |
| 75 else | |
| 76 echo "<td>$one</td>" >> "$html" | |
| 77 fi | |
| 78 echo "<td>$read_count1</td>" >> "$html" | |
| 79 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 80 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html" | |
| 81 else | |
| 82 echo "<td>$two</td>" >> "$html" | |
| 83 fi | |
| 84 echo "<td>$read_count2</td>" >> "$html" | |
| 85 echo "<td>$sum</td>" >> "$html" | |
| 86 echo "<td>${percent}%</td>" >> "$html" | |
| 87 echo "</tr>" >> "$html" | |
| 88 oldLocus="$locus" | |
| 89 if [ "${cut_off_value}" == "0" ] ; then | |
| 90 scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /></td>" | |
| 91 fi | |
| 92 done < tmp.txt | |
| 93 echo "</tbody></table>" >> "$html" | |
| 94 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html" | |
| 95 echo "</div>" >> "$html" | |
| 96 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html" | |
| 97 echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html" | |
| 98 echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html" | |
| 99 echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html" | |
| 100 echo "${scatterplot_tab}</tr></table></div>" >> "$html" | |
| 101 | |
| 102 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt | |
| 103 echo "<div class='tabbertab' title='Data reads'>" >> "$html" | |
| 104 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" | |
| 105 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html" | |
| 106 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" | |
| 107 echo "<tbody>" >> "$html" | |
| 108 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>" | |
| 109 while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2 | |
| 110 do | |
| 111 if [ "$locus" != "$oldLocus" ] ; then | |
| 112 echo "<tr><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td><td></td></tr><tr>" >> "$html" | |
| 113 echo "<tr><td><b>$locus</b></td>" >> "$html" | |
| 114 else | |
| 115 echo "<td></td>" >> "$html" | |
| 116 fi | |
| 117 echo "<td>$v_segment</td>" >> "$html" | |
| 118 echo "<td>$j_segment</td>" >> "$html" | |
| 119 echo "<td>>$cut_off_value</td>" >> "$html" | |
| 120 if [ "$both" != "0" ] ; then | |
| 121 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$both</td>" >> "$html" | |
| 122 else | |
| 123 echo "<td>$both</td>" >> "$html" | |
| 124 fi | |
| 125 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 126 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html" | |
| 127 else | |
| 128 echo "<td>$one</td>" >> "$html" | |
| 129 fi | |
| 130 echo "<td>$read_count1</td>" >> "$html" | |
| 131 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 132 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html" | |
| 133 else | |
| 134 echo "<td>$two</td>" >> "$html" | |
| 135 fi | |
| 136 echo "<td>$read_count2</td>" >> "$html" | |
| 137 echo "<td>$sum</td>" >> "$html" | |
| 138 echo "<td>${percent}%</td>" >> "$html" | |
| 139 echo "</tr>" >> "$html" | |
| 140 oldLocus="$locus" | |
| 141 if [ "${cut_off_value}" == "0" ] ; then | |
| 142 scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /></td>" | |
| 143 fi | |
| 144 done < tmp.txt | |
| 145 echo "</tbody></table>" >> "$html" | |
| 146 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html" | |
| 147 echo "</div>" >> "$html" | |
| 148 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html" | |
| 149 echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> "$html" | |
| 150 echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> "$html" | |
| 151 echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html" | |
| 152 echo "${scatterplot_tab}</tr></table></div>" >> "$html" | |
| 153 echo "</div>" >> "$html" | |
| 154 echo "</div>" >> "$html" | |
| 155 echo "</html>" >> "$html" | |
| 156 done < patients.txt | |
| 157 | |
| 158 html="index.html" | |
| 159 echo "<html>" > $html | |
| 160 echo "<table>" >> "$html" | |
| 161 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>" >> "$html" | |
| 162 for patient in "${singles[@]}" | |
| 163 do | |
| 164 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html" | |
| 165 done | |
| 166 echo "<tr><td><b>Pairs (Left & Right):</b></td></tr>" >> "$html" | |
| 167 for patient in "${pairs_Left_Right[@]}" | |
| 168 do | |
| 169 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html" | |
| 170 done | |
| 171 echo "<tr><td><b>Pairs (BM & PB):</b></td></tr>" >> "$html" | |
| 172 for patient in "${pairs_BM_PB[@]}" | |
| 173 do | |
| 174 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html" | |
| 175 done | |
| 176 echo "<tr><td><b>Pairs (Dx & R):</b></td></tr>" >> "$html" | |
| 177 for patient in "${pairs_R_Dx[@]}" | |
| 178 do | |
| 179 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "$html" | |
| 180 done | |
| 181 echo "<tr><td><b>Triplets:</b></td></tr>" >> "$html" | |
| 182 | |
| 183 while read sample1 sample2 sample3 | |
| 184 do | |
| 185 sample1="$(echo ${sample1} | tr -d '\r' | tr -d '\n')" | |
| 186 sample2="$(echo ${sample2} | tr -d '\r' | tr -d '\n')" | |
| 187 sample3="$(echo ${sample3} | tr -d '\r' | tr -d '\n')" | |
| 188 patient="${sample1}_${sample2}_${sample3}" | |
| 189 echo "$patient" | |
| 190 html="${patient}.html" | |
| 191 echo "<tr><td><a href='${patient}.html'>$patient</a></td></tr>" >> "index.html" | |
| 192 echo "$header" > $html | |
| 193 oldLocus="" | |
| 194 tail -n+2 ${patient}_freq.txt | sed "s/>//" > tmp.txt | |
| 195 echo "<div class='tabber'>" >> "$html" | |
| 196 echo "<div class='tabbertab' title='Data frequency'>" >> "$html" | |
| 197 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" | |
| 198 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html" | |
| 199 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>" >> "$html" | |
| 200 echo "<tbody>" >> "$html" | |
| 201 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>" | |
| 202 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three | |
| 203 do | |
| 204 if [ "$locus" != "$oldLocus" ] ; then | |
| 205 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>" >> "$html" | |
| 206 echo "<tr><td><b>$locus</b></td>" >> "$html" | |
| 207 else | |
| 208 echo "<td></td>" >> "$html" | |
| 209 fi | |
| 210 echo "<td>$v_segment</td>" >> "$html" | |
| 211 echo "<td>$j_segment</td>" >> "$html" | |
| 212 echo "<td>>$cut_off_value</td>" >> "$html" | |
| 213 if [ "$all" != "0" ] ; then | |
| 214 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$all</td>" >> "$html" | |
| 215 else | |
| 216 echo "<td>$all</td>" >> "$html" | |
| 217 fi | |
| 218 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 219 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$one</td>" >> "$html" | |
| 220 else | |
| 221 echo "<td>$one</td>" >> "$html" | |
| 222 fi | |
| 223 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 224 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$two</td>" >> "$html" | |
| 225 else | |
| 226 echo "<td>$two</td>" >> "$html" | |
| 227 fi | |
| 228 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 229 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"freq\")'>$three</td>" >> "$html" | |
| 230 else | |
| 231 echo "<td>$three</td>" >> "$html" | |
| 232 fi | |
| 233 | |
| 234 if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 235 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${one_two}</td>" >> "$html" | |
| 236 else | |
| 237 echo "<td>${one_two}</td>" >> "$html" | |
| 238 fi | |
| 239 if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 240 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${one_three}</td>" >> "$html" | |
| 241 else | |
| 242 echo "<td>${one_three}</td>" >> "$html" | |
| 243 fi | |
| 244 if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 245 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}freq.txt\", \"$patient\", \"freq\")'>${two_three}</td>" >> "$html" | |
| 246 else | |
| 247 echo "<td>${two_three}</td>" >> "$html" | |
| 248 fi | |
| 249 | |
| 250 echo "</tr>" >> "$html" | |
| 251 oldLocus="$locus" | |
| 252 if [ "${cut_off_value}" == "0" ] ; then | |
| 253 scatterplot_tab="${scatterplot_tab}<td><img src='${sample1}_${sample2}_${sample3}_freq_${locus}_scatter.png' /></td>" | |
| 254 fi | |
| 255 done < tmp.txt | |
| 256 echo "</tbody></table>" >> "$html" | |
| 257 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_freq'></div></td></tr></table>" >> "$html" | |
| 258 echo "</div>" >> "$html" | |
| 259 echo "<div class='tabbertab' title='Graphs frequency'>" >> "$html" | |
| 260 echo "<a href='${patient}_freq_total_all.png'><img src='${patient}_freq_total_all.png' width='1280' height='720' /></a><br />" >> "$html" | |
| 261 echo "<a href='${patient}_freq_indiv_all.png'><img src='${patient}_freq_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html" | |
| 262 echo "${scatterplot_tab}</tr></table></div>" >> "$html" | |
| 263 | |
| 264 tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt | |
| 265 echo "<div class='tabbertab' title='Data reads'>" >> "$html" | |
| 266 echo "<table><tr><td style='vertical-align:top;'>" >> "$html" | |
| 267 echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html" | |
| 268 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>" >> "$html" | |
| 269 echo "<tbody>" >> "$html" | |
| 270 scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>" | |
| 271 while read locus j_segment v_segment cut_off_value all one two three one_two one_three two_three | |
| 272 do | |
| 273 if [ "$locus" != "$oldLocus" ] ; then | |
| 274 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>" >> "$html" | |
| 275 echo "<tr><td><b>$locus</b></td>" >> "$html" | |
| 276 else | |
| 277 echo "<td></td>" >> "$html" | |
| 278 fi | |
| 279 echo "<td>$v_segment</td>" >> "$html" | |
| 280 echo "<td>$j_segment</td>" >> "$html" | |
| 281 echo "<td>>$cut_off_value</td>" >> "$html" | |
| 282 if [ "$all" != "0" ] ; then | |
| 283 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$all</td>" >> "$html" | |
| 284 else | |
| 285 echo "<td>$all</td>" >> "$html" | |
| 286 fi | |
| 287 if [ "$one" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 288 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$one</td>" >> "$html" | |
| 289 else | |
| 290 echo "<td>$one</td>" >> "$html" | |
| 291 fi | |
| 292 if [ "$two" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 293 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$two</td>" >> "$html" | |
| 294 else | |
| 295 echo "<td>$two</td>" >> "$html" | |
| 296 fi | |
| 297 if [ "$three" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 298 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample3}_${locus}_${cut_off_value}.txt\", \"$patient\", \"reads\")'>$three</td>" >> "$html" | |
| 299 else | |
| 300 echo "<td>$three</td>" >> "$html" | |
| 301 fi | |
| 302 | |
| 303 if [ "${one_two}" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 304 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample2}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${one_two}</td>" >> "$html" | |
| 305 else | |
| 306 echo "<td>${one_two}</td>" >> "$html" | |
| 307 fi | |
| 308 if [ "${one_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 309 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample1}_${sample3}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${one_three}</td>" >> "$html" | |
| 310 else | |
| 311 echo "<td>${one_three}</td>" >> "$html" | |
| 312 fi | |
| 313 if [ "${two_three}" != "0" ] && [ "$cut_off_value" != "0" ] ; then | |
| 314 echo "<td data-patient='${patient}' style='cursor:pointer' onclick='javascript:loadfile(\"${sample2}_${sample3}_${locus}_${cut_off_value}reads.txt\", \"$patient\", \"reads\")'>${two_three}</td>" >> "$html" | |
| 315 else | |
| 316 echo "<td>${two_three}</td>" >> "$html" | |
| 317 fi | |
| 318 | |
| 319 echo "</tr>" >> "$html" | |
| 320 oldLocus="$locus" | |
| 321 if [ "${cut_off_value}" == "0" ] ; then | |
| 322 scatterplot_tab="${scatterplot_tab}<td><img src='${sample1}_${sample2}_${sample3}_reads_${locus}_scatter.png' /></td>" | |
| 323 fi | |
| 324 done < tmp.txt | |
| 325 echo "</tbody></table>" >> "$html" | |
| 326 echo "</td><td style='vertical-align:top;'><div id='result_div_${patient}_reads'></div></td></tr></table>" >> "$html" | |
| 327 echo "</div>" >> "$html" | |
| 328 echo "<div class='tabbertab' title='Graphs reads'>" >> "$html" | |
| 329 echo "<a href='${patient}_reads_total_all.png'><img src='${patient}_reads_total_all.png' width='1280' height='720' /></a><br />" >> "$html" | |
| 330 echo "<a href='${patient}_reads_indiv_all.png'><img src='${patient}_reads_indiv_all.png' width='1280' height='720' /></a><br /></div>" >> "$html" | |
| 331 echo "${scatterplot_tab}</tr></table></div>" >> "$html" | |
| 332 echo "</div>" >> "$html" | |
| 333 echo "</div>" >> "$html" | |
| 334 echo "</html>" >> "$html" | |
| 335 done < triplets.txt | |
| 336 rm tmp.txt | |
| 337 | |
| 338 | |
| 339 html="index.html" | |
| 340 | |
| 341 echo "</table>" >> "$html" | |
| 342 echo "<a href='log.html'>log</a><br />" >> "$html" | |
| 343 echo "<a href='single_matches.html'>single_matches</a><br />" >> "$html" | |
| 344 echo "<a href='multiple_matches.html'>multiple_matches</a><br />" >> "$html" | |
| 345 echo "</html>" >> "$html" | |
| 346 | |
| 347 cp "index.html" "$outputFile" | |
| 348 |