|
5
|
1 #!/bin/bash
|
|
|
2
|
|
|
3 inputFile=$1
|
|
|
4 outputDir=$3
|
|
|
5 outputFile=$3/index.html #$2
|
|
|
6 clonalType=$4
|
|
|
7 species=$5
|
|
|
8 locus=$6
|
|
|
9 filterproductive=$7
|
|
|
10 clonality_method=$8
|
|
|
11
|
|
|
12 dir="$(cd "$(dirname "$0")" && pwd)"
|
|
|
13 useD="false"
|
|
|
14 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then
|
|
|
15 echo "species D region in reference db"
|
|
|
16 useD="true"
|
|
|
17 fi
|
|
|
18 echo "$species"
|
|
|
19 if [[ "$species" == *"custom"* ]] ; then
|
|
|
20 loci=(${locus//;/ })
|
|
|
21 useD="true"
|
|
|
22 echo "${loci[@]}"
|
|
|
23 if [[ "${#loci[@]}" -eq "2" ]] ; then
|
|
|
24 useD="false"
|
|
|
25 fi
|
|
|
26 fi
|
|
|
27 mkdir $3
|
|
|
28 cp $dir/genes.txt $outputDir
|
|
|
29 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1
|
|
|
30 cp $dir/tabber.js $outputDir
|
|
|
31 cp $dir/style.css $outputDir
|
|
|
32 cp $dir/script.js $outputDir
|
|
|
33 cp $dir/jquery-1.11.0.min.js $outputDir
|
|
|
34 cp $dir/pure-min.css $outputDir
|
|
17
|
35 cp $dir/IGH_junctie_analyse.png $outputDir
|
|
5
|
36 samples=`cat $outputDir/samples.txt`
|
|
|
37
|
|
|
38 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)<br />" > $2
|
|
|
39 echo "<table border = 1>" >> $2
|
|
19
|
40 echo "<thead><tr><th>Donor/Replicate</th><th>All</th><th>Productive</th><th>Unique Productive</th><th>Unproductive</th><th>Unique Unproductive</th></tr></thead>" >> $2
|
|
5
|
41 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un
|
|
|
42 do
|
|
|
43 echo "<tr><td>$sample</td>" >> $2
|
|
|
44 echo "<td>$all</td>" >> $2
|
|
|
45 echo "<td>$productive (${perc_prod}%)</td>" >> $2
|
|
|
46 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2
|
|
|
47 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2
|
|
|
48 echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2
|
|
|
49 done < $outputDir/productive_counting.txt
|
|
18
|
50 echo "</table><br />" >> $2
|
|
19
|
51 echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate. <br />" >> $2
|
|
18
|
52 echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2
|
|
|
53 echo "</center></html>" >> $2
|
|
5
|
54
|
|
|
55 echo "<html><head><title>Report on:" >> $outputFile
|
|
|
56
|
|
|
57 mkdir $outputDir/circos
|
|
|
58 cp $dir/circos/* $outputDir/circos/
|
|
|
59 #CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
|
|
|
60 #CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
|
|
|
61
|
|
|
62 #CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
|
|
|
63 #CIRCOSDIR="/home/galaxy/Anaconda3/bin"
|
|
|
64
|
|
|
65 USECIRCOS="no"
|
|
|
66 if [ -d "$CIRCOSDIR" ]; then
|
|
|
67 USECIRCOS="yes"
|
|
|
68 else
|
|
12
|
69 if [ -d "/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/" ]; then #hopefully temporary fix
|
|
5
|
70 USECIRCOS="yes"
|
|
|
71 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools"
|
|
|
72 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
|
|
|
73 fi
|
|
12
|
74
|
|
24
|
75 if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix #or not
|
|
12
|
76 USECIRCOS="yes"
|
|
|
77 CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
|
|
|
78 CIRCOSDIR="/home/galaxy/Anaconda3/bin"
|
|
|
79 fi
|
|
5
|
80 fi
|
|
12
|
81
|
|
5
|
82 echo "Using Circos: $USECIRCOS"
|
|
|
83 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf
|
|
|
84 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output
|
|
|
85 echo " $sample" >> $outputFile
|
|
|
86
|
|
|
87 if [[ "$USECIRCOS" != "yes" ]]; then
|
|
|
88 continue
|
|
|
89 fi
|
|
|
90
|
|
|
91 circos_file="$outputDir/${sample}_VJ_circos.txt"
|
|
|
92 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
|
|
|
93 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
|
|
|
94 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
|
|
|
95 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png
|
|
36
|
96 mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg
|
|
5
|
97
|
|
|
98
|
|
|
99 if [[ "$useD" == "true" ]] ; then
|
|
|
100 circos_file="$outputDir/${sample}_VD_circos.txt"
|
|
|
101 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
|
|
|
102 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
|
|
|
103 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
|
|
|
104 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png
|
|
36
|
105 mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg
|
|
5
|
106
|
|
|
107 circos_file="$outputDir/${sample}_DJ_circos.txt"
|
|
|
108 echo -e -n "labels$(cat ${circos_file})" > ${circos_file}
|
|
|
109 cat "${circos_file}" | $CIRCOSTOOLS/tableviewer/bin/parse-table -configfile $dir/circos/parse-table.conf 2>&1 | $CIRCOSTOOLS/tableviewer/bin/make-conf -dir $outputDir/circos/
|
|
|
110 $CIRCOSDIR/circos -conf $outputDir/circos/circos.conf 2>&1
|
|
|
111 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
|
|
36
|
112 mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg
|
|
5
|
113 fi
|
|
|
114 done
|
|
|
115 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
|
|
|
116 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $outputFile
|
|
|
117 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
|
|
|
118 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
|
|
|
119 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
|
|
|
120 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
|
|
|
121
|
|
8
|
122
|
|
32
|
123 echo "<a href='VFPlot.pdf'><img src='VFPlot.png'/></a>" >> $outputFile
|
|
5
|
124 if [[ "$useD" == "true" ]] ; then
|
|
32
|
125 echo "<a href='DFPlot.pdf'><img src='DFPlot.png'/></a>" >> $outputFile
|
|
5
|
126 fi
|
|
32
|
127 echo "<a href='VPlot.pdf'><img src='VPlot.png'/></a>" >> $outputFile
|
|
5
|
128 if [[ "$useD" == "true" ]] ; then
|
|
32
|
129 echo "<a href='DPlot.pdf'><img src='DPlot.png'/></a>" >> $outputFile
|
|
5
|
130 fi
|
|
32
|
131 echo "<a href='JPlot.pdf'><img src='JPlot.png'/></a> <br />" >> $outputFile
|
|
24
|
132
|
|
32
|
133 echo "<a href='DReadingFrame.pdf'><img src='DReadingFrame.png'/></a>" >> $outputFile
|
|
18
|
134
|
|
|
135 cat $dir/naive_gene_freq.htm >> $outputFile
|
|
|
136
|
|
8
|
137 echo "</div>" >> $outputFile
|
|
|
138
|
|
|
139 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile
|
|
32
|
140 echo "<a href='CDR3LengthPlot.pdf'><img src='CDR3LengthPlot.png'/></a><br />" >> $outputFile
|
|
|
141 echo "<a href='AAComposition.pdf'><img src='AAComposition.png'/></a>" >> $outputFile
|
|
24
|
142
|
|
8
|
143
|
|
|
144 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
|
|
19
|
145 echo "<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
|
|
24
|
146 while read Sample median
|
|
8
|
147 do
|
|
|
148 echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile
|
|
24
|
149 done < $outputDir/AAMedianBySample.txt
|
|
8
|
150 echo "</table>" >> $outputFile
|
|
|
151
|
|
18
|
152 cat $dir/naive_cdr3_char.htm >> $outputFile
|
|
|
153
|
|
5
|
154 echo "</div>" >> $outputFile
|
|
|
155
|
|
|
156 #Heatmaps
|
|
|
157
|
|
|
158 count=1
|
|
|
159 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
|
|
|
160 for sample in $samples; do
|
|
|
161 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
|
|
|
162 if [[ "$useD" == "true" ]] ; then
|
|
32
|
163 echo "<td><a href='HeatmapVD_$sample.pdf'><img src='HeatmapVD_$sample.png'/></a></td>" >> $outputFile
|
|
5
|
164 fi
|
|
32
|
165 echo "<td><a href='HeatmapVJ_$sample.pdf'><img src='HeatmapVJ_$sample.png'/></a></td>" >> $outputFile
|
|
5
|
166 if [[ "$useD" == "true" ]] ; then
|
|
32
|
167 echo "<td><a href='HeatmapDJ_$sample.pdf'><img src='HeatmapDJ_$sample.png'/></a></td>" >> $outputFile
|
|
5
|
168 fi
|
|
|
169 echo "</tr></table></div>" >> $outputFile
|
|
|
170 count=$((count+1))
|
|
|
171 done
|
|
18
|
172
|
|
|
173 cat $dir/naive_heatmap.htm >> $outputFile
|
|
|
174
|
|
5
|
175 echo "</div></div>" >> $outputFile
|
|
|
176
|
|
18
|
177 echo "<div class='tabbertab' title='Compare Heatmaps'><table class='pure-table pure-table-striped'><thead><tr><th>ID</th><th>Include</th></tr></thead>" >> $outputFile
|
|
|
178 for sample in $samples; do
|
|
|
179 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
|
|
|
180 done
|
|
|
181 echo "</table><div name='comparisonarea'>" >> $outputFile
|
|
|
182 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
|
|
|
183 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
|
|
|
184 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
|
|
|
185
|
|
|
186 cat $dir/naive_compare.htm >> $outputFile
|
|
|
187
|
|
|
188 echo "</div></div>" >> $outputFile
|
|
|
189
|
|
|
190
|
|
5
|
191 #circos
|
|
|
192
|
|
|
193 if [[ "$USECIRCOS" == "yes" ]]; then
|
|
|
194
|
|
|
195 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile
|
|
|
196 for sample in $samples; do
|
|
|
197 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile
|
|
|
198 if [[ "$useD" == "true" ]] ; then
|
|
35
|
199 echo "<tr><td>V-D</td><td><a href='circosVD_${sample}.svg'><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
|
|
5
|
200 fi
|
|
35
|
201 echo "<tr><td>V-J</td><td><a href='circosVJ_${sample}.svg'><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
|
|
5
|
202 if [[ "$useD" == "true" ]] ; then
|
|
35
|
203 echo "<tr><td>D-J</td><td><a href='circosDJ_${sample}.svg'><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile
|
|
5
|
204 fi
|
|
|
205 echo "<center></table></div>" >> $outputFile
|
|
|
206 count=$((count+1))
|
|
|
207 done
|
|
18
|
208
|
|
|
209 cat $dir/naive_circos.htm >> $outputFile
|
|
|
210
|
|
5
|
211 echo "</div></div>" >> $outputFile
|
|
|
212 fi
|
|
|
213 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile
|
|
|
214
|
|
|
215 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
|
|
|
216 echo "$hasReplicateColumn"
|
|
|
217 #if its a 'new' merged file with replicate info
|
|
17
|
218 if [[ "$hasReplicateColumn" == "Yes" && "${clonality_method}" != "none" ]] ; then
|
|
|
219 if [[ "${clonality_method}" == "boyd" ]] ; then
|
|
|
220 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
|
|
|
221 else
|
|
|
222 echo "<div class='tabbertab' title='Shared Clonal Types'><div class='tabber'>" >> $outputFile
|
|
|
223 fi
|
|
|
224
|
|
5
|
225 for sample in $samples; do
|
|
|
226 echo "${clonality_method}"
|
|
26
|
227
|
|
|
228 echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
|
|
|
229
|
|
|
230 if [[ "${clonality_method}" == "boyd" ]] ; then
|
|
22
|
231 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.txt)"
|
|
26
|
232 echo "<tr><td>Clonality Score: </td><td>$clonalityScore</td></tr>" >> $outputFile
|
|
5
|
233 fi
|
|
26
|
234
|
|
|
235 #replicate,reads,squared
|
|
|
236 echo "<tr><td>Replicate ID</td><td>Number of Sequences</td></tr>" >> $outputFile
|
|
|
237 while read replicate reads squared
|
|
|
238 do
|
|
|
239 echo "<tr><td>$replicate</td><td>$reads</td></tr>" >> $outputFile
|
|
|
240 done < $outputDir/ReplicateReads_$sample.txt
|
|
|
241
|
|
|
242 #sum of reads and reads squared
|
|
|
243 while read readsSum squaredSum
|
|
|
244 do
|
|
|
245 echo "<tr><td>Sum</td><td>$readsSum</td></tr>" >> $outputFile
|
|
|
246 done < $outputDir/ReplicateSumReads_$sample.txt
|
|
|
247
|
|
|
248 echo "<tr><td></td><td></td></tr>" >> $outputFile
|
|
|
249
|
|
|
250 #overview
|
|
|
251 echo "<tr><td>Number of replicates containing the coincidence</td><td>Number of sequences shared between replicates</td></tr>" >> $outputFile
|
|
|
252 while read type count weight weightedCount
|
|
|
253 do
|
|
|
254 if [[ "$type" -eq "1" ]]; then
|
|
|
255 echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile
|
|
|
256 else
|
|
|
257 echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td></tr>" >> $outputFile
|
|
|
258 fi
|
|
|
259 done < $outputDir/ClonalityOverView_$sample.txt
|
|
|
260 echo "</table></div>" >> $outputFile
|
|
5
|
261 done
|
|
18
|
262
|
|
|
263 cat $dir/naive_clonality.htm >> $outputFile
|
|
|
264
|
|
5
|
265 echo "</div></div>" >> $outputFile
|
|
|
266 fi
|
|
|
267
|
|
|
268 #hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
|
|
|
269
|
|
|
270 #if [[ "$hasJunctionData" == "Yes" ]] ; then
|
|
24
|
271 if [ -a "$outputDir/junctionAnalysisProd_mean_wD.txt" ] ; then
|
|
5
|
272 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
|
|
17
|
273 echo "<img src='IGH_junctie_analyse.png' />" >> $outputFile
|
|
|
274
|
|
24
|
275 echo "<center><p style='font-size: 20;'>Unique rearrangements with a V, D and J gene assigned</p></center>" >> $outputFile
|
|
38
|
276 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
|
|
24
|
277 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
|
|
5
|
278 do
|
|
|
279 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
|
|
24
|
280 done < $outputDir/junctionAnalysisProd_mean_wD.txt
|
|
5
|
281 echo "</tbody></table>" >> $outputFile
|
|
|
282
|
|
38
|
283 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
|
|
24
|
284 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
|
|
5
|
285 do
|
|
26
|
286 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
|
|
24
|
287 done < $outputDir/junctionAnalysisUnProd_mean_wD.txt
|
|
5
|
288 echo "</tbody></table>" >> $outputFile
|
|
|
289
|
|
38
|
290 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
|
|
24
|
291 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
|
|
5
|
292 do
|
|
|
293 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
|
|
24
|
294 done < $outputDir/junctionAnalysisProd_median_wD.txt
|
|
5
|
295 echo "</tbody></table>" >> $outputFile
|
|
|
296
|
|
38
|
297 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.D</th><th>D.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
|
|
24
|
298 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
|
|
5
|
299 do
|
|
26
|
300 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELD</td><td>$DDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
|
|
24
|
301 done < $outputDir/junctionAnalysisUnProd_median_wD.txt
|
|
|
302 echo "</tbody></table>" >> $outputFile
|
|
|
303
|
|
|
304 # again for no-d
|
|
|
305 echo "<center><p style='font-size: 20;'>Unique rearrangements with only a V and J gene assigned</p></center>" >> $outputFile
|
|
38
|
306 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
|
|
24
|
307 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
|
|
|
308 do
|
|
|
309 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
|
|
|
310 done < $outputDir/junctionAnalysisProd_mean_nD.txt
|
|
|
311 echo "</tbody></table>" >> $outputFile
|
|
|
312
|
|
38
|
313 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
|
|
24
|
314 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
|
|
|
315 do
|
|
26
|
316 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
|
|
24
|
317 done < $outputDir/junctionAnalysisUnProd_mean_nD.txt
|
|
|
318 echo "</tbody></table>" >> $outputFile
|
|
|
319
|
|
38
|
320 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
|
|
24
|
321 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
|
|
|
322 do
|
|
|
323 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>$median</td></tr>" >> $outputFile
|
|
|
324 done < $outputDir/junctionAnalysisProd_median_nD.txt
|
|
|
325 echo "</tbody></table>" >> $outputFile
|
|
|
326
|
|
38
|
327 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Donor</th><th>Number of sequences</th><th>V.DEL</th><th>P1</th><th>N</th><th>P2</th><th>DEL.J</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><th>CDR3.Length</th><thead></tr><tbody>" >> $outputFile
|
|
24
|
328 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
|
|
|
329 do
|
|
27
|
330 echo "<tr><td>$Sample</td><td>$unique</td><td>$VDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELJ</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td><td>-</td></tr>" >> $outputFile
|
|
24
|
331 done < $outputDir/junctionAnalysisUnProd_median_nD.txt
|
|
5
|
332 echo "</tbody></table>" >> $outputFile
|
|
|
333
|
|
18
|
334 cat $dir/naive_junction.htm >> $outputFile
|
|
|
335
|
|
5
|
336 echo "</div>" >> $outputFile
|
|
|
337 fi
|
|
|
338
|
|
|
339 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
|
|
|
340 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
|
|
|
341 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
|
|
18
|
342 echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile
|
|
24
|
343 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>" >> $outputFile
|
|
5
|
344
|
|
18
|
345 echo "<tr><td>The dataset used to generate the distribution of V gene families graph</td><td><a href='VFFrequency.txt'>Download</a></td></tr>" >> $outputFile
|
|
5
|
346 if [[ "$useD" == "true" ]] ; then
|
|
18
|
347 echo "<tr><td>The dataset used to generate the distribution of D gene families graph</td><td><a href='DFFrequency.txt'>Download</a></td></tr>" >> $outputFile
|
|
5
|
348 fi
|
|
|
349
|
|
18
|
350 echo "<tr><td>The dataset used to generate the relative frequency of V gene usage graph</td><td><a href='VFrequency.txt'>Download</a></td></tr>" >> $outputFile
|
|
5
|
351 if [[ "$useD" == "true" ]] ; then
|
|
18
|
352 echo "<tr><td>The dataset used to generate the relative frequency of D gene usage graph</td><td><a href='DFrequency.txt'>Download</a></td></tr>" >> $outputFile
|
|
5
|
353 fi
|
|
18
|
354 echo "<tr><td>The dataset used to generate the relative frequency of J gene usage graph</td><td><a href='JFrequency.txt'>Download</a></td></tr>" >> $outputFile
|
|
24
|
355 echo "<tr><td>The dataset used to generate the relative frequency of the D reading frame graph</td><td><a href='DReadingFrame.txt'>Download</a></td></tr>" >> $outputFile
|
|
|
356
|
|
|
357 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CDR3 Characteristics</td></tr>" >> $outputFile
|
|
|
358 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.txt'>Download</a></td></tr>" >> $outputFile
|
|
18
|
359 echo "<tr><td>The dataset used to generate the Amino Acid Composition in the CDR3 graph</td><td><a href='AAComposition.txt'>Download</a></td></tr>" >> $outputFile
|
|
5
|
360
|
|
24
|
361 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Heatmaps</td></tr>" >> $outputFile
|
|
5
|
362 for sample in $samples; do
|
|
|
363 if [[ "$useD" == "true" ]] ; then
|
|
24
|
364 echo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href='HeatmapVD_$sample.txt'>Download</a></td></tr>" >> $outputFile
|
|
5
|
365 fi
|
|
24
|
366 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.txt'>Download</a></td></tr>" >> $outputFile
|
|
5
|
367 if [[ "$useD" == "true" ]] ; then
|
|
24
|
368 echo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href='HeatmapDJ_$sample.txt'>Download</a></td></tr>" >> $outputFile
|
|
5
|
369 fi
|
|
|
370 done
|
|
|
371
|
|
24
|
372 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Circos</td></tr>" >> $outputFile
|
|
|
373 for sample in $samples; do
|
|
|
374 if [[ "$useD" == "true" ]] ; then
|
|
|
375 echo "<tr><td>The data used to generate the VD Circos plots for $sample.</td><td><a href='${sample}_VD_circos.txt'>Download</a></td></tr>" >> $outputFile
|
|
|
376 fi
|
|
|
377 echo "<tr><td>The data used to generate the VJ Circos plots for $sample.</td><td><a href='${sample}_VJ_circos.txt'>Download</a></td></tr>" >> $outputFile
|
|
|
378 if [[ "$useD" == "true" ]] ; then
|
|
|
379 echo "<tr><td>The data used to generate the DJ Circos plots for $sample.</td><td><a href='${sample}_DJ_circos.txt'>Download</a></td></tr>" >> $outputFile
|
|
|
380 fi
|
|
|
381 done
|
|
|
382
|
|
|
383 #echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile
|
|
|
384
|
|
|
385 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $outputFile
|
|
|
386 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.txt'>Download</a></td></tr>" >> $outputFile
|
|
25
|
387 echo "<tr><td>Sequences that are present in more than one replicate</td><td><a href='clonaltypes_replicates.txt'>Download</a></td></tr>" >> $outputFile
|
|
5
|
388
|
|
|
389 echo "</table>" >> $outputFile
|
|
18
|
390
|
|
|
391 cat $dir/naive_downloads.htm >> $outputFile
|
|
|
392
|
|
5
|
393 echo "</div></html>" >> $outputFile
|
