|
0
|
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
|
