Mercurial > repos > davidvanzessen > argalaxy_tools
annotate report_clonality/r_wrapper.sh @ 58:4c6df851e262 draft default tip
"planemo upload commit 1a7731bb4fe2e80fb1fdc88121783068af3edb08"
| author | rhpvorderman |
|---|---|
| date | Fri, 21 Apr 2023 10:04:39 +0000 |
| parents | 33412e85e669 |
| children |
| 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=$8 | |
| 11 | |
|
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33412e85e669
"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
rhpvorderman
parents:
54
diff
changeset
|
12 ALL_OUTPUTS_ZIP="$outputDir/all_outputs.zip" |
|
33412e85e669
"planemo upload commit 2a9ed3adf321f18047c3746735a5e79a4586798d"
rhpvorderman
parents:
54
diff
changeset
|
13 |
| 53 | 14 dir="$(cd "$(dirname "$0")" && pwd)" |
| 15 useD="false" | |
| 16 if grep -q "$species.*${locus}D" "$dir/genes.txt" ; then | |
| 17 echo "species D region in reference db" | |
| 18 useD="true" | |
| 19 fi | |
| 20 echo "$species" | |
| 21 if [[ "$species" == *"custom"* ]] ; then | |
|
54
81b3eb11ed2c
"planemo upload commit 6c0195cc4de6a34e2c46d875be4fc2157a21cdf6"
rhpvorderman
parents:
53
diff
changeset
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22 loci=("${locus//;/ }") |
| 53 | 23 useD="true" |
| 24 echo "${loci[@]}" | |
| 25 if [[ "${#loci[@]}" -eq "2" ]] ; then | |
| 26 useD="false" | |
| 27 fi | |
| 28 fi | |
| 29 mkdir $3 | |
| 30 cp $dir/genes.txt $outputDir | |
| 31 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType "$species" "$locus" $filterproductive ${clonality_method} 2>&1 | |
| 32 cp $dir/tabber.js $outputDir | |
| 33 cp $dir/style.css $outputDir | |
| 34 cp $dir/script.js $outputDir | |
| 35 cp $dir/jquery-1.11.0.min.js $outputDir | |
| 36 cp $dir/pure-min.css $outputDir | |
| 37 cp $dir/IGH_junctie_analyse.png $outputDir | |
| 38 samples=`cat $outputDir/samples.txt` | |
| 39 | |
| 40 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 | |
| 41 echo "<table border = 1>" >> $2 | |
| 42 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>" >> $2 | |
| 43 while IFS=, read sample all productive perc_prod productive_unique perc_prod_un unproductive perc_unprod unproductive_unique perc_unprod_un | |
| 44 do | |
| 45 echo "<tr><td>$sample</td>" >> $2 | |
| 46 echo "<td>$all</td>" >> $2 | |
| 47 if [[ "$productive" != "0" ]] ; then | |
| 48 echo "<td>$productive (${perc_prod}%)</td>" >> $2 | |
| 49 echo "<td>$productive_unique (${perc_prod_un}%)</td>" >> $2 | |
| 50 echo "<td>$unproductive (${perc_unprod}%)</td>" >> $2 | |
| 51 echo "<td>$unproductive_unique (${perc_unprod_un}%)</td></tr>" >> $2 | |
| 52 else | |
| 53 echo "<td colspan='4' style='background-color: red;'>No productive sequences!</td>" >> $2 | |
| 54 fi | |
| 55 done < $outputDir/productive_counting.txt | |
| 56 echo "</table><br />" >> $2 | |
| 57 echo "Table showing the number and percentage of (unique) productive and unproductive sequences per donor and per replicate. <br />" >> $2 | |
| 58 echo "The definition of unique sequences is based on the clonal type definition filter setting chosen. " >> $2 | |
| 59 echo "</center></html>" >> $2 | |
| 60 | |
| 61 echo "<html><head><title>Report on:" >> $outputFile | |
| 62 | |
| 63 mkdir $outputDir/circos | |
| 64 cp -R $dir/circos/* $outputDir/circos/ | |
| 65 | |
| 66 USECIRCOS="no" | |
| 67 path_to_circos=$(which circos) | |
| 68 if [ -x "$path_to_circos" ]; then | |
| 69 USECIRCOS="yes" | |
| 70 fi | |
| 71 | |
| 72 echo "Using Circos: $USECIRCOS" | |
| 73 sed -i "s%DATA_DIR%$outputDir/circos%" $outputDir/circos/circos.conf | |
| 74 for sample in $samples; do #output the samples to a file and create the circos plots with the R script output | |
| 75 echo " $sample" >> $outputFile | |
| 76 | |
| 77 if [[ "$USECIRCOS" != "yes" ]]; then | |
| 78 continue | |
| 79 fi | |
| 80 | |
| 81 circos_file="$outputDir/${sample}_VJ_circos.txt" | |
| 82 sed -i -- 's%/%:%g' $circos_file | |
| 83 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} | |
| 84 echo "Circos tools command:" | |
| 85 echo "cat \"${circos_file}\" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/" | |
| 86 cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/ | |
| 87 | |
| 88 echo "Circos command:" | |
| 89 echo "circos -conf $outputDir/circos/circos.conf 2>&1" | |
| 90 circos -conf $outputDir/circos/circos.conf 2>&1 | |
| 91 mv $outputDir/circos/circos.png $outputDir/circosVJ_${sample}.png | |
| 92 mv $outputDir/circos/circos.svg $outputDir/circosVJ_${sample}.svg | |
| 93 | |
| 94 | |
| 95 if [[ "$useD" == "true" ]] ; then | |
| 96 circos_file="$outputDir/${sample}_VD_circos.txt" | |
| 97 sed -i -- 's%/%:%g' $circos_file | |
| 98 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} | |
| 99 cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/ | |
| 100 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt | |
| 101 circos -conf $outputDir/circos/circos.conf 2>&1 | |
| 102 mv $outputDir/circos/circos.png $outputDir/circosVD_${sample}.png | |
| 103 mv $outputDir/circos/circos.svg $outputDir/circosVD_${sample}.svg | |
| 104 | |
| 105 circos_file="$outputDir/${sample}_DJ_circos.txt" | |
| 106 sed -i -- 's%/%:%g' $circos_file | |
| 107 echo -e -n "labels$(cat ${circos_file})" > ${circos_file} | |
| 108 cat "${circos_file}" | parse-table -configfile $dir/circos/parse-table.conf 2>&1 | make-conf -dir $outputDir/circos/ | |
| 109 sed -i -- 's%/%:%g' $outputDir/circos/cells.txt | |
| 110 circos -conf $outputDir/circos/circos.conf 2>&1 | |
| 111 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png | |
| 112 mv $outputDir/circos/circos.svg $outputDir/circosDJ_${sample}.svg | |
| 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 | |
| 122 | |
| 123 echo "<a href='VFPlot.pdf'><img src='VFPlot.png'/></a>" >> $outputFile | |
| 124 if [[ "$useD" == "true" ]] ; then | |
| 125 echo "<a href='DFPlot.pdf'><img src='DFPlot.png'/></a>" >> $outputFile | |
| 126 fi | |
| 127 echo "<a href='VPlot.pdf'><img src='VPlot.png'/></a>" >> $outputFile | |
| 128 if [[ "$useD" == "true" ]] ; then | |
| 129 echo "<a href='DPlot.pdf'><img src='DPlot.png'/></a>" >> $outputFile | |
| 130 fi | |
| 131 echo "<a href='JPlot.pdf'><img src='JPlot.png'/></a> <br />" >> $outputFile | |
| 132 | |
| 133 echo "<a href='DReadingFrame.pdf'><img src='DReadingFrame.png'/></a>" >> $outputFile | |
| 134 | |
| 135 cat $dir/naive_gene_freq.htm >> $outputFile | |
| 136 | |
| 137 echo "</div>" >> $outputFile | |
| 138 | |
| 139 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile | |
| 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 | |
| 142 | |
| 143 | |
| 144 echo "<table class='pure-table pure-table-striped'>" >> $outputFile | |
| 145 echo "<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile | |
| 146 while read Sample median | |
| 147 do | |
| 148 echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile | |
| 149 done < $outputDir/AAMedianBySample.txt | |
| 150 echo "</table>" >> $outputFile | |
| 151 | |
| 152 cat $dir/naive_cdr3_char.htm >> $outputFile | |
| 153 | |
| 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 | |
| 163 echo "<td><a href='HeatmapVD_$sample.pdf'><img src='HeatmapVD_$sample.png'/></a></td>" >> $outputFile | |
| 164 fi | |
| 165 echo "<td><a href='HeatmapVJ_$sample.pdf'><img src='HeatmapVJ_$sample.png'/></a></td>" >> $outputFile | |
| 166 if [[ "$useD" == "true" ]] ; then | |
| 167 echo "<td><a href='HeatmapDJ_$sample.pdf'><img src='HeatmapDJ_$sample.png'/></a></td>" >> $outputFile | |
| 168 fi | |
| 169 echo "</tr></table></div>" >> $outputFile | |
| 170 count=$((count+1)) | |
| 171 done | |
| 172 | |
| 173 cat $dir/naive_heatmap.htm >> $outputFile | |
| 174 | |
| 175 echo "</div></div>" >> $outputFile | |
| 176 | |
| 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>" >> $outputFile | |
| 189 | |
| 190 | |
| 191 #circos | |
| 192 | |
| 193 if [[ "$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 | |
| 199 echo "<tr><td>V-D</td><td><a href='circosVD_${sample}.svg'><img src='circosVD_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile | |
| 200 fi | |
| 201 echo "<tr><td>V-J</td><td><a href='circosVJ_${sample}.svg'><img src='circosVJ_${sample}.png' width='700' height='700'/></td></tr>" >> $outputFile | |
| 202 if [[ "$useD" == "true" ]] ; then | |
| 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 | |
| 204 fi | |
| 205 echo "<center></table></div>" >> $outputFile | |
| 206 count=$((count+1)) | |
| 207 done | |
| 208 | |
| 209 cat $dir/naive_circos.htm >> $outputFile | |
| 210 | |
| 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 | |
| 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 | |
| 225 for sample in $samples; do | |
| 226 echo "${clonality_method}" | |
| 227 | |
| 228 echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile | |
| 229 | |
| 230 if [[ "${clonality_method}" == "boyd" ]] ; then | |
| 231 clonalityScore="$(cat $outputDir/lymphclon_clonality_${sample}.txt)" | |
| 232 echo "<tr><td>Clonality Score: </td><td>$clonalityScore</td></tr>" >> $outputFile | |
| 233 fi | |
| 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 | |
| 261 done | |
| 262 | |
| 263 cat $dir/naive_clonality.htm >> $outputFile | |
| 264 | |
| 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 | |
| 271 if [ -a "$outputDir/junctionAnalysisProd_mean_wD.txt" ] ; then | |
| 272 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile | |
| 273 echo "<img src='IGH_junctie_analyse.png' />" >> $outputFile | |
| 274 | |
| 275 echo "<center><p style='font-size: 20;'>Unique rearrangements with a V, D and J gene assigned</p></center>" >> $outputFile | |
| 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>" >> $outputFile | |
| 277 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median | |
| 278 do | |
| 279 echo "<tr><td>$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 | |
| 280 done < $outputDir/junctionAnalysisProd_mean_wD.txt | |
| 281 echo "</tbody></table>" >> $outputFile | |
| 282 | |
| 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>" >> $outputFile | |
| 284 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median | |
| 285 do | |
| 286 echo "<tr><td>$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 | |
| 287 done < $outputDir/junctionAnalysisUnProd_mean_wD.txt | |
| 288 echo "</tbody></table>" >> $outputFile | |
| 289 | |
| 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>" >> $outputFile | |
| 291 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median | |
| 292 do | |
| 293 echo "<tr><td>$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 | |
| 294 done < $outputDir/junctionAnalysisProd_median_wD.txt | |
| 295 echo "</tbody></table>" >> $outputFile | |
| 296 | |
| 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>" >> $outputFile | |
| 298 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median | |
| 299 do | |
| 300 echo "<tr><td>$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 | |
| 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 | |
| 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>" >> $outputFile | |
| 307 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median | |
| 308 do | |
| 309 echo "<tr><td>$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 | |
| 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>" >> $outputFile | |
| 314 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median | |
| 315 do | |
| 316 echo "<tr><td>$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 | |
| 317 done < $outputDir/junctionAnalysisUnProd_mean_nD.txt | |
| 318 echo "</tbody></table>" >> $outputFile | |
| 319 | |
| 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>" >> $outputFile | |
| 321 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median | |
| 322 do | |
| 323 echo "<tr><td>$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 | |
| 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>" >> $outputFile | |
| 328 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median | |
| 329 do | |
| 330 echo "<tr><td>$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 | |
| 331 done < $outputDir/junctionAnalysisUnProd_median_nD.txt | |
| 332 echo "</tbody></table>" >> $outputFile | |
| 333 | |
| 334 cat $dir/naive_junction.htm >> $outputFile | |
| 335 | |
| 336 echo "</div>" >> $outputFile | |
| 337 fi | |
| 338 | |
|
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339 |
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340 # Create zip file with all download files |
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341 # Use 7za as it is packaged in the container already. |
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342 cd "$outputDir" || exit 1 |
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343 |
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344 7za a -tzip "$ALL_OUTPUTS_ZIP" -- \ |
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345 allUnique.txt VFFrequency.txt VFrequency.txt \ |
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346 JFrequency.txt DReadingFrame.txt CDR3LengthPlot.txt \ |
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347 AAComposition.txt clonalityComplete.txt |
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348 |
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349 if [[ "$useD" == "true" ]] ; then |
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350 7za a -tzip "$ALL_OUTPUTS_ZIP" -- \ |
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351 DFFrequency.txt DFrequency.txt |
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352 fi |
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353 for sample in $samples; do |
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354 if [[ "$useD" == "true" ]] ; then |
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355 7za a -tzip "$ALL_OUTPUTS_ZIP" -- \ |
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356 "HeatmapVD_$sample.txt" "HeatmapDJ_$sample.txt" \ |
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357 "${sample}_VD_circos.txt" "${sample}_DJ_circos.txt" |
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358 fi |
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359 7za a -tzip "$ALL_OUTPUTS_ZIP" -- \ |
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360 "HeatmapVJ_$sample.txt" "${sample}_VJ_circos.txt" |
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361 done |
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362 |
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363 cd $dir || exit 1 |
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364 |
| 53 | 365 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile |
| 366 echo "<table class='pure-table pure-table-striped'>" >> $outputFile | |
| 367 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile | |
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368 echo "<tr><td>All outputs below in a zip file</td><td><a href='all_outputs.zip'>Download</a></td></tr>" >> $outputFile |
| 53 | 369 echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile |
| 370 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>" >> $outputFile | |
| 371 | |
| 372 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>" >> $outputFile | |
| 373 if [[ "$useD" == "true" ]] ; then | |
| 374 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 | |
| 375 fi | |
| 376 | |
| 377 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>" >> $outputFile | |
| 378 if [[ "$useD" == "true" ]] ; then | |
| 379 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 | |
| 380 fi | |
| 381 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 | |
| 382 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 | |
| 383 | |
| 384 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CDR3 Characteristics</td></tr>" >> $outputFile | |
| 385 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.txt'>Download</a></td></tr>" >> $outputFile | |
| 386 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 | |
| 387 | |
| 388 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Heatmaps</td></tr>" >> $outputFile | |
| 389 for sample in $samples; do | |
| 390 if [[ "$useD" == "true" ]] ; then | |
| 391 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 | |
| 392 fi | |
| 393 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.txt'>Download</a></td></tr>" >> $outputFile | |
| 394 if [[ "$useD" == "true" ]] ; then | |
| 395 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 | |
| 396 fi | |
| 397 done | |
| 398 | |
| 399 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Circos</td></tr>" >> $outputFile | |
| 400 for sample in $samples; do | |
| 401 if [[ "$useD" == "true" ]] ; then | |
| 402 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 | |
| 403 fi | |
| 404 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>" >> $outputFile | |
| 405 if [[ "$useD" == "true" ]] ; then | |
| 406 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 | |
| 407 fi | |
| 408 done | |
| 409 | |
| 410 #echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile | |
| 411 | |
| 412 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $outputFile | |
| 413 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 | |
| 414 # echo "<tr><td>Sequences that are present in more than one replicate</td><td><a href='clonaltypes_replicates.txt'>Download</a></td></tr>" >> $outputFile | |
| 415 | |
| 416 echo "</table>" >> $outputFile | |
| 417 | |
| 418 cat $dir/naive_downloads.htm >> $outputFile | |
| 419 | |
| 420 echo "</div></html>" >> $outputFile |