Mercurial > repos > davidvanzessen > argalaxy_tools
annotate report_clonality/r_wrapper.sh @ 54:81b3eb11ed2c draft
"planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
| author | rhpvorderman |
|---|---|
| date | Tue, 16 Nov 2021 15:42:32 +0000 |
| parents | 0ef7f80ea061 |
| children | 33412e85e669 |
| rev | line source |
|---|---|
| 53 | 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 | |
|
54
81b3eb11ed2c
"planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents:
53
diff
changeset
|
20 loci=("${locus//;/ }") |
| 53 | 21 useD="true" |
| 22 echo "${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 | |
| 35 cp $dir/IGH_junctie_analyse.png $outputDir | |
| 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 | |
| 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>" >> $2 | |
| 41 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un | |
| 42 do | |
| 43 echo "<tr><td>$sample</td>" >> $2 | |
| 44 echo "<td>$all</td>" >> $2 | |
| 45 if [[ "$productive" != "0" ]] ; then | |
| 46 echo "<td>$productive (${perc_prod}%)</td>" >> $2 | |
| 47 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2 | |
| 48 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2 | |
| 49 echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2 | |
| 50 else | |
| 51 echo "<td colspan='4' style='background-color: red;'>No productive sequences!</td>" >> $2 | |
| 52 fi | |
| 53 done < $outputDir/productive_counting.txt | |
| 54 echo "</table><br />" >> $2 | |
| 55 echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate. <br />" >> $2 | |
| 56 echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2 | |
| 57 echo "</center></html>" >> $2 | |
| 58 | |
| 59 echo "<html><head><title>Report on:" >> $outputFile | |
| 60 | |
| 61 mkdir $outputDir/circos | |
| 62 cp -R $dir/circos/* $outputDir/circos/ | |
| 63 | |
| 64 USECIRCOS="no" | |
| 65 path_to_circos=$(which circos) | |
| 66 if [ -x "$path_to_circos" ]; then | |
| 67 USECIRCOS="yes" | |
| 68 fi | |
| 69 | |
| 70 echo "Using Circos: $USECIRCOS" | |
| 71 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf | |
| 72 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output | |
| 73 echo " $sample" >> $outputFile | |
| 74 | |
| 75 if [[ "$USECIRCOS" != "yes" ]]; then | |
| 76 continue | |
| 77 fi | |
| 78 | |
| 79 circos_file="$outputDir/${sample}_VJ_circos.txt" | |
| 80 sed -i -- 's%/%:%g' $circos_file | |
| 81 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} | |
| 82 echo "Circos tools command:" | |
| 83 echo "cat \"${circos_file}\" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/" | |
| 84 cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/ | |
| 85 | |
| 86 echo "Circos command:" | |
| 87 echo "circos -conf $outputDir/circos/circos.conf 2>&1" | |
| 88 circos -conf $outputDir/circos/circos.conf 2>&1 | |
| 89 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png | |
| 90 mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg | |
| 91 | |
| 92 | |
| 93 if [[ "$useD" == "true" ]] ; then | |
| 94 circos_file="$outputDir/${sample}_VD_circos.txt" | |
| 95 sed -i -- 's%/%:%g' $circos_file | |
| 96 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} | |
| 97 cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/ | |
| 98 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt | |
| 99 circos -conf $outputDir/circos/circos.conf 2>&1 | |
| 100 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png | |
| 101 mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg | |
| 102 | |
| 103 circos_file="$outputDir/${sample}_DJ_circos.txt" | |
| 104 sed -i -- 's%/%:%g' $circos_file | |
| 105 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} | |
| 106 cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/ | |
| 107 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt | |
| 108 circos -conf $outputDir/circos/circos.conf 2>&1 | |
| 109 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png | |
| 110 mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg | |
| 111 fi | |
| 112 done | |
| 113 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile | |
| 114 echo "<link rel='stylesheet' type='text/css' href='pure-min.css'>" >> $outputFile | |
| 115 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile | |
| 116 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile | |
| 117 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile | |
| 118 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile | |
| 119 | |
| 120 | |
| 121 echo "<a href='VFPlot.pdf'><img src='VFPlot.png'/></a>" >> $outputFile | |
| 122 if [[ "$useD" == "true" ]] ; then | |
| 123 echo "<a href='DFPlot.pdf'><img src='DFPlot.png'/></a>" >> $outputFile | |
| 124 fi | |
| 125 echo "<a href='VPlot.pdf'><img src='VPlot.png'/></a>" >> $outputFile | |
| 126 if [[ "$useD" == "true" ]] ; then | |
| 127 echo "<a href='DPlot.pdf'><img src='DPlot.png'/></a>" >> $outputFile | |
| 128 fi | |
| 129 echo "<a href='JPlot.pdf'><img src='JPlot.png'/></a> <br />" >> $outputFile | |
| 130 | |
| 131 echo "<a href='DReadingFrame.pdf'><img src='DReadingFrame.png'/></a>" >> $outputFile | |
| 132 | |
| 133 cat $dir/naive_gene_freq.htm >> $outputFile | |
| 134 | |
| 135 echo "</div>" >> $outputFile | |
| 136 | |
| 137 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile | |
| 138 echo "<a href='CDR3LengthPlot.pdf'><img src='CDR3LengthPlot.png'/></a><br />" >> $outputFile | |
| 139 echo "<a href='AAComposition.pdf'><img src='AAComposition.png'/></a>" >> $outputFile | |
| 140 | |
| 141 | |
| 142 echo "<table class='pure-table pure-table-striped'>" >> $outputFile | |
| 143 echo "<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile | |
| 144 while read Sample median | |
| 145 do | |
| 146 echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile | |
| 147 done < $outputDir/AAMedianBySample.txt | |
| 148 echo "</table>" >> $outputFile | |
| 149 | |
| 150 cat $dir/naive_cdr3_char.htm >> $outputFile | |
| 151 | |
| 152 echo "</div>" >> $outputFile | |
| 153 | |
| 154 #Heatmaps | |
| 155 | |
| 156 count=1 | |
| 157 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile | |
| 158 for sample in $samples; do | |
| 159 echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile | |
| 160 if [[ "$useD" == "true" ]] ; then | |
| 161 echo "<td><a href='HeatmapVD_$sample.pdf'><img src='HeatmapVD_$sample.png'/></a></td>" >> $outputFile | |
| 162 fi | |
| 163 echo "<td><a href='HeatmapVJ_$sample.pdf'><img src='HeatmapVJ_$sample.png'/></a></td>" >> $outputFile | |
| 164 if [[ "$useD" == "true" ]] ; then | |
| 165 echo "<td><a href='HeatmapDJ_$sample.pdf'><img src='HeatmapDJ_$sample.png'/></a></td>" >> $outputFile | |
| 166 fi | |
| 167 echo "</tr></table></div>" >> $outputFile | |
| 168 count=$((count+1)) | |
| 169 done | |
| 170 | |
| 171 cat $dir/naive_heatmap.htm >> $outputFile | |
| 172 | |
| 173 echo "</div></div>" >> $outputFile | |
| 174 | |
| 175 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 | |
| 176 for sample in $samples; do | |
| 177 echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile | |
| 178 done | |
| 179 echo "</table><div name='comparisonarea'>" >> $outputFile | |
| 180 echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile | |
| 181 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile | |
| 182 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile | |
| 183 | |
| 184 cat $dir/naive_compare.htm >> $outputFile | |
| 185 | |
| 186 echo "</div></div>" >> $outputFile | |
| 187 | |
| 188 | |
| 189 #circos | |
| 190 | |
| 191 if [[ "$USECIRCOS" == "yes" ]]; then | |
| 192 | |
| 193 echo "<div class='tabbertab' title='Circos'><div class='tabber'>" >> $outputFile | |
| 194 for sample in $samples; do | |
| 195 echo "<div class='tabbertab' title='$sample'><table border='1'><center>" >> $outputFile | |
| 196 if [[ "$useD" == "true" ]] ; then | |
| 197 echo "<tr><td>V-D</td><td><a href='circosVD_${sample}.svg'><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile | |
| 198 fi | |
| 199 echo "<tr><td>V-J</td><td><a href='circosVJ_${sample}.svg'><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile | |
| 200 if [[ "$useD" == "true" ]] ; then | |
| 201 echo "<tr><td>D-J</td><td><a href='circosDJ_${sample}.svg'><img src='circosDJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile | |
| 202 fi | |
| 203 echo "<center></table></div>" >> $outputFile | |
| 204 count=$((count+1)) | |
| 205 done | |
| 206 | |
| 207 cat $dir/naive_circos.htm >> $outputFile | |
| 208 | |
| 209 echo "</div></div>" >> $outputFile | |
| 210 fi | |
| 211 #echo "<div class='tabbertab' title='Interactive'><svg class='chart'></svg><script src='http://d3js.org/d3.v3.min.js'></script></div>" >> $outputFile | |
| 212 | |
| 213 hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)" | |
| 214 echo "$hasReplicateColumn" | |
| 215 #if its a 'new' merged file with replicate info | |
| 216 if [[ "$hasReplicateColumn" == "Yes" && "${clonality_method}" != "none" ]] ; then | |
| 217 if [[ "${clonality_method}" == "boyd" ]] ; then | |
| 218 echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile | |
| 219 else | |
| 220 echo "<div class='tabbertab' title='Shared Clonal Types'><div class='tabber'>" >> $outputFile | |
| 221 fi | |
| 222 | |
| 223 for sample in $samples; do | |
| 224 echo "${clonality_method}" | |
| 225 | |
| 226 echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile | |
| 227 | |
| 228 if [[ "${clonality_method}" == "boyd" ]] ; then | |
| 229 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.txt)" | |
| 230 echo "<tr><td>Clonality Score: </td><td>$clonalityScore</td></tr>" >> $outputFile | |
| 231 fi | |
| 232 | |
| 233 #replicate,reads,squared | |
| 234 echo "<tr><td>Replicate ID</td><td>Number of Sequences</td></tr>" >> $outputFile | |
| 235 while read replicate reads squared | |
| 236 do | |
| 237 echo "<tr><td>$replicate</td><td>$reads</td></tr>" >> $outputFile | |
| 238 done < $outputDir/ReplicateReads_$sample.txt | |
| 239 | |
| 240 #sum of reads and reads squared | |
| 241 while read readsSum squaredSum | |
| 242 do | |
| 243 echo "<tr><td>Sum</td><td>$readsSum</td></tr>" >> $outputFile | |
| 244 done < $outputDir/ReplicateSumReads_$sample.txt | |
| 245 | |
| 246 echo "<tr><td></td><td></td></tr>" >> $outputFile | |
| 247 | |
| 248 #overview | |
| 249 echo "<tr><td>Number of replicates containing the coincidence</td><td>Number of sequences shared between replicates</td></tr>" >> $outputFile | |
| 250 while read type count weight weightedCount | |
| 251 do | |
| 252 if [[ "$type" -eq "1" ]]; then | |
| 253 echo "<tr><td>$type</td><td>$count</td></tr>" >> $outputFile | |
| 254 else | |
| 255 echo "<tr><td><a href='coincidences_${sample}_${type}.txt'>$type</a></td><td>$count</td></tr>" >> $outputFile | |
| 256 fi | |
| 257 done < $outputDir/ClonalityOverView_$sample.txt | |
| 258 echo "</table></div>" >> $outputFile | |
| 259 done | |
| 260 | |
| 261 cat $dir/naive_clonality.htm >> $outputFile | |
| 262 | |
| 263 echo "</div></div>" >> $outputFile | |
| 264 fi | |
| 265 | |
| 266 #hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)" | |
| 267 | |
| 268 #if [[ "$hasJunctionData" == "Yes" ]] ; then | |
| 269 if [ -a "$outputDir/junctionAnalysisProd_mean_wD.txt" ] ; then | |
| 270 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile | |
| 271 echo "<img src='IGH_junctie_analyse.png' />" >> $outputFile | |
| 272 | |
| 273 echo "<center><p style='font-size: 20;'>Unique rearrangements with a V, D and J gene assigned</p></center>" >> $outputFile | |
| 274 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>" >> $outputFile | |
| 275 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median | |
| 276 do | |
| 277 echo "<tr><td>$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 | |
| 278 done < $outputDir/junctionAnalysisProd_mean_wD.txt | |
| 279 echo "</tbody></table>" >> $outputFile | |
| 280 | |
| 281 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>" >> $outputFile | |
| 282 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median | |
| 283 do | |
| 284 echo "<tr><td>$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 | |
| 285 done < $outputDir/junctionAnalysisUnProd_mean_wD.txt | |
| 286 echo "</tbody></table>" >> $outputFile | |
| 287 | |
| 288 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>" >> $outputFile | |
| 289 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median | |
| 290 do | |
| 291 echo "<tr><td>$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 | |
| 292 done < $outputDir/junctionAnalysisProd_median_wD.txt | |
| 293 echo "</tbody></table>" >> $outputFile | |
| 294 | |
| 295 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>" >> $outputFile | |
| 296 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median | |
| 297 do | |
| 298 echo "<tr><td>$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 | |
| 299 done < $outputDir/junctionAnalysisUnProd_median_wD.txt | |
| 300 echo "</tbody></table>" >> $outputFile | |
| 301 | |
| 302 # again for no-d | |
| 303 echo "<center><p style='font-size: 20;'>Unique rearrangements with only a V and J gene assigned</p></center>" >> $outputFile | |
| 304 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>" >> $outputFile | |
| 305 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median | |
| 306 do | |
| 307 echo "<tr><td>$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 | |
| 308 done < $outputDir/junctionAnalysisProd_mean_nD.txt | |
| 309 echo "</tbody></table>" >> $outputFile | |
| 310 | |
| 311 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>" >> $outputFile | |
| 312 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median | |
| 313 do | |
| 314 echo "<tr><td>$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 | |
| 315 done < $outputDir/junctionAnalysisUnProd_mean_nD.txt | |
| 316 echo "</tbody></table>" >> $outputFile | |
| 317 | |
| 318 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>" >> $outputFile | |
| 319 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median | |
| 320 do | |
| 321 echo "<tr><td>$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 | |
| 322 done < $outputDir/junctionAnalysisProd_median_nD.txt | |
| 323 echo "</tbody></table>" >> $outputFile | |
| 324 | |
| 325 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>" >> $outputFile | |
| 326 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median | |
| 327 do | |
| 328 echo "<tr><td>$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 | |
| 329 done < $outputDir/junctionAnalysisUnProd_median_nD.txt | |
| 330 echo "</tbody></table>" >> $outputFile | |
| 331 | |
| 332 cat $dir/naive_junction.htm >> $outputFile | |
| 333 | |
| 334 echo "</div>" >> $outputFile | |
| 335 fi | |
| 336 | |
| 337 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile | |
| 338 echo "<table class='pure-table pure-table-striped'>" >> $outputFile | |
| 339 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile | |
| 340 echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile | |
| 341 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>" >> $outputFile | |
| 342 | |
| 343 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>" >> $outputFile | |
| 344 if [[ "$useD" == "true" ]] ; then | |
| 345 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 | |
| 346 fi | |
| 347 | |
| 348 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>" >> $outputFile | |
| 349 if [[ "$useD" == "true" ]] ; then | |
| 350 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 | |
| 351 fi | |
| 352 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 | |
| 353 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 | |
| 354 | |
| 355 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CDR3 Characteristics</td></tr>" >> $outputFile | |
| 356 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.txt'>Download</a></td></tr>" >> $outputFile | |
| 357 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 | |
| 358 | |
| 359 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Heatmaps</td></tr>" >> $outputFile | |
| 360 for sample in $samples; do | |
| 361 if [[ "$useD" == "true" ]] ; then | |
| 362 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 | |
| 363 fi | |
| 364 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.txt'>Download</a></td></tr>" >> $outputFile | |
| 365 if [[ "$useD" == "true" ]] ; then | |
| 366 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 | |
| 367 fi | |
| 368 done | |
| 369 | |
| 370 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Circos</td></tr>" >> $outputFile | |
| 371 for sample in $samples; do | |
| 372 if [[ "$useD" == "true" ]] ; then | |
| 373 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 | |
| 374 fi | |
| 375 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>" >> $outputFile | |
| 376 if [[ "$useD" == "true" ]] ; then | |
| 377 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 | |
| 378 fi | |
| 379 done | |
| 380 | |
| 381 #echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile | |
| 382 | |
| 383 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $outputFile | |
| 384 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 | |
| 385 # echo "<tr><td>Sequences that are present in more than one replicate</td><td><a href='clonaltypes_replicates.txt'>Download</a></td></tr>" >> $outputFile | |
| 386 | |
| 387 echo "</table>" >> $outputFile | |
| 388 | |
| 389 cat $dir/naive_downloads.htm >> $outputFile | |
| 390 | |
| 391 echo "</div></html>" >> $outputFile |