Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 24:d5d203d38c8a draft

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Uploaded
author davidvanzessen
date Wed, 01 Feb 2017 09:48:38 -0500
parents e2fbdfacec1d
children 94765af0db1f
comparison
equal deleted inserted replaced
23:e2fbdfacec1d 24:d5d203d38c8a
70 USECIRCOS="yes" 70 USECIRCOS="yes"
71 CIRCOSTOOLS="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/circos-tools-0.21/tools" 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/" 72 CIRCOSDIR="/data/galaxy/galaxy-dist/toolsheddependencies/circos/0.64/saskia-hiltemann/cg_circos_plots/bbfdd52d64fd/bin/"
73 fi 73 fi
74 74
75 if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix 75 if [ -d "/home/galaxy/Anaconda3/bin" ]; then #hopefully temporary fix #or not
76 USECIRCOS="yes" 76 USECIRCOS="yes"
77 CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools" 77 CIRCOSTOOLS="/home/galaxy/circos/circos-tools-0.22/tools"
78 CIRCOSDIR="/home/galaxy/Anaconda3/bin" 78 CIRCOSDIR="/home/galaxy/Anaconda3/bin"
79 fi 79 fi
80 fi 80 fi
124 fi 124 fi
125 echo "<img src='VPlot.png'/>" >> $outputFile 125 echo "<img src='VPlot.png'/>" >> $outputFile
126 if [[ "$useD" == "true" ]] ; then 126 if [[ "$useD" == "true" ]] ; then
127 echo "<img src='DPlot.png'/>" >> $outputFile 127 echo "<img src='DPlot.png'/>" >> $outputFile
128 fi 128 fi
129 echo "<img src='JPlot.png'/>" >> $outputFile 129 echo "<img src='JPlot.png'/> <br />" >> $outputFile
130
131 echo "<img src='DReadingFrame.png'/>" >> $outputFile
130 132
131 cat $dir/naive_gene_freq.htm >> $outputFile 133 cat $dir/naive_gene_freq.htm >> $outputFile
132 134
133 echo "</div>" >> $outputFile 135 echo "</div>" >> $outputFile
134 136
135 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile 137 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile
136 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile 138 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
137 echo "<img src='AAComposition.png'/>" >> $outputFile 139 echo "<img src='AAComposition.png'/>" >> $outputFile
138 echo "<img src='DReadingFrame.png'/>" >> $outputFile 140
139 141
140 echo "<table class='pure-table pure-table-striped'>" >> $outputFile 142 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
141 echo "<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile 143 echo "<thead><tr><th>Donor</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
142 while IFS=, read Sample median 144 while read Sample median
143 do 145 do
144 echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile 146 echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile
145 done < $outputDir/AAMedianBySample.csv 147 done < $outputDir/AAMedianBySample.txt
146 echo "</table>" >> $outputFile 148 echo "</table>" >> $outputFile
147 149
148 cat $dir/naive_cdr3_char.htm >> $outputFile 150 cat $dir/naive_cdr3_char.htm >> $outputFile
149 151
150 echo "</div>" >> $outputFile 152 echo "</div>" >> $outputFile
276 fi 278 fi
277 279
278 #hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)" 280 #hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
279 281
280 #if [[ "$hasJunctionData" == "Yes" ]] ; then 282 #if [[ "$hasJunctionData" == "Yes" ]] ; then
281 if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then 283 if [ -a "$outputDir/junctionAnalysisProd_mean_wD.txt" ] ; then
282 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile 284 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
283 echo "<img src='IGH_junctie_analyse.png' />" >> $outputFile 285 echo "<img src='IGH_junctie_analyse.png' />" >> $outputFile
284 286
287 echo "<center><p style='font-size: 20;'>Unique rearrangements with a V, D and J gene assigned</p></center>" >> $outputFile
285 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile 288 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
286 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median 289 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
287 do 290 do
288 echo "<tr><td>$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>" >> $outputFile 291 echo "<tr><td>$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
289 done < $outputDir/junctionAnalysisProd_mean.csv 292 done < $outputDir/junctionAnalysisProd_mean_wD.txt
290 echo "</tbody></table>" >> $outputFile 293 echo "</tbody></table>" >> $outputFile
291 294
292 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile 295 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
293 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median 296 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
294 do 297 do
295 echo "<tr><td>$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>" >> $outputFile 298 echo "<tr><td>$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>$median</td></tr>" >> $outputFile
296 done < $outputDir/junctionAnalysisUnProd_mean.csv 299 done < $outputDir/junctionAnalysisUnProd_mean_wD.txt
297 echo "</tbody></table>" >> $outputFile 300 echo "</tbody></table>" >> $outputFile
298 301
299 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile 302 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
300 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median 303 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
301 do 304 do
302 echo "<tr><td>$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>" >> $outputFile 305 echo "<tr><td>$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
303 done < $outputDir/junctionAnalysisProd_median.csv 306 done < $outputDir/junctionAnalysisProd_median_wD.txt
304 echo "</tbody></table>" >> $outputFile 307 echo "</tbody></table>" >> $outputFile
305 308
306 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile 309 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
307 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median 310 while read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP median
308 do 311 do
309 echo "<tr><td>$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>" >> $outputFile 312 echo "<tr><td>$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
310 done < $outputDir/junctionAnalysisUnProd_median.csv 313 done < $outputDir/junctionAnalysisUnProd_median_wD.txt
314 echo "</tbody></table>" >> $outputFile
315
316 # again for no-d
317 echo "<center><p style='font-size: 20;'>Unique rearrangements with only a V and J gene assigned</p></center>" >> $outputFile
318 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>Median.CDR3</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_mean_nD.txt
323 echo "</tbody></table>" >> $outputFile
324
325 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>Median.CDR3</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>$TotalP</td><td>$median</td></tr>" >> $outputFile
329 done < $outputDir/junctionAnalysisUnProd_mean_nD.txt
330 echo "</tbody></table>" >> $outputFile
331
332 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
333 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
334 do
335 echo "<tr><td>$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
336 done < $outputDir/junctionAnalysisProd_median_nD.txt
337 echo "</tbody></table>" >> $outputFile
338
339 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>Median.CDR3</th><thead></tr><tbody>" >> $outputFile
340 while read Sample unique VDEL P1 N1 P2 DELJ TotalDel TotalN TotalP median
341 do
342 echo "<tr><td>$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
343 done < $outputDir/junctionAnalysisUnProd_median_nD.txt
311 echo "</tbody></table>" >> $outputFile 344 echo "</tbody></table>" >> $outputFile
312 345
313 cat $dir/naive_junction.htm >> $outputFile 346 cat $dir/naive_junction.htm >> $outputFile
314 347
315 echo "</div>" >> $outputFile 348 echo "</div>" >> $outputFile
317 350
318 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile 351 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
319 echo "<table class='pure-table pure-table-striped'>" >> $outputFile 352 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
320 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile 353 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
321 echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile 354 echo "<tr><td>The filtered dataset</td><td><a href='allUnique.txt'>Download</a></td></tr>" >> $outputFile
322 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 355 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Gene frequencies</td></tr>" >> $outputFile
323
324 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
325 356
326 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 357 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>" >> $outputFile
327 if [[ "$useD" == "true" ]] ; then 358 if [[ "$useD" == "true" ]] ; then
328 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 359 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
329 fi 360 fi
331 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 362 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>" >> $outputFile
332 if [[ "$useD" == "true" ]] ; then 363 if [[ "$useD" == "true" ]] ; then
333 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 364 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
334 fi 365 fi
335 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 366 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
367 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
368
369 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>CDR3 Characteristics</td></tr>" >> $outputFile
370 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.txt'>Download</a></td></tr>" >> $outputFile
336 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 371 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
337 372
373 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Heatmaps</td></tr>" >> $outputFile
338 for sample in $samples; do 374 for sample in $samples; do
339 if [[ "$useD" == "true" ]] ; then 375 if [[ "$useD" == "true" ]] ; then
340 echo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href='HeatmapVD_$sample.csv'>Download</a></td></tr>" >> $outputFile 376 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
341 fi 377 fi
342 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile 378 echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.txt'>Download</a></td></tr>" >> $outputFile
343 if [[ "$useD" == "true" ]] ; then 379 if [[ "$useD" == "true" ]] ; then
344 echo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href='HeatmapDJ_$sample.csv'>Download</a></td></tr>" >> $outputFile 380 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
345 fi 381 fi
346 done 382 done
347 383
348 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 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Circos</td></tr>" >> $outputFile
385 for sample in $samples; do
386 if [[ "$useD" == "true" ]] ; then
387 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
388 fi
389 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>" >> $outputFile
390 if [[ "$useD" == "true" ]] ; then
391 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
392 fi
393 done
394
395 #echo "<tr><td>A frequency count of V Gene + J Gene + CDR3</td><td><a href='VJCDR3_count.txt'>Download</a></td></tr>" >> $outputFile
396
397 echo "<tr><td colspan='2' style='background-color:#E0E0E0;'>Clonality</td></tr>" >> $outputFile
398 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
349 399
350 echo "</table>" >> $outputFile 400 echo "</table>" >> $outputFile
351 401
352 cat $dir/naive_downloads.htm >> $outputFile 402 cat $dir/naive_downloads.htm >> $outputFile
353 403