Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 70:6fdafffd7f0f draft

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author davidvanzessen
date Wed, 17 Aug 2016 08:16:55 -0400
parents a59de79f6c0f
children 55d06821d6a5
comparison
equal deleted inserted replaced
69:a59de79f6c0f 70:6fdafffd7f0f
87 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png 87 mv $outputDir/circos/circos.png $outputDir/circosDJ_${sample}.png
88 88
89 fi 89 fi
90 done 90 done
91 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile 91 echo "</title><script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
92 echo "<link rel='stylesheet' href='http://yui.yahooapis.com/pure/0.6.0/pure-min.css'>" >> $outputFile
92 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile 93 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
93 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile 94 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
94 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile 95 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
95 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile 96 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
96 97
156 for sample in $samples; do 157 for sample in $samples; do
157 echo "${clonality_method}" 158 echo "${clonality_method}"
158 if [[ "${clonality_method}" == "old" ]] ; then 159 if [[ "${clonality_method}" == "old" ]] ; then
159 echo "in old" 160 echo "in old"
160 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)" 161 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
161 echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile 162 echo "<div class='tabbertab' title='$sample'><table class='pure-table pure-table-striped'>" >> $outputFile
162 echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile 163 echo "<thead><tr><th colspan='4'>Clonality Score: $clonalityScore</th></tr></thead>" >> $outputFile
163 164
164 #replicate,reads,squared 165 #replicate,reads,squared
165 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile 166 echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
166 while IFS=, read replicate reads squared 167 while IFS=, read replicate reads squared
167 do 168 do
205 #hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)" 206 #hasJunctionData="$(if head -n 1 $inputFile | grep -qE '3V.REGION.trimmed.nt.nb'; then echo 'Yes'; else echo 'No'; fi)"
206 207
207 #if [[ "$hasJunctionData" == "Yes" ]] ; then 208 #if [[ "$hasJunctionData" == "Yes" ]] ; then
208 if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then 209 if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then
209 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile 210 echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile
210 echo "<table border='1' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile 211 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive mean</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile
211 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP 212 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP
212 do 213 do
213 echo "<tr><td>$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></tr>" >> $outputFile 214 echo "<tr><td>$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></tr>" >> $outputFile
214 done < $outputDir/junctionAnalysisProd_mean.csv 215 done < $outputDir/junctionAnalysisProd_mean.csv
215 echo "</tbody></table>" >> $outputFile 216 echo "</tbody></table>" >> $outputFile
216 217
217 echo "<table border='1' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile 218 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive mean</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile
218 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP 219 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP
219 do 220 do
220 echo "<tr><td>$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></tr>" >> $outputFile 221 echo "<tr><td>$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></tr>" >> $outputFile
221 done < $outputDir/junctionAnalysisUnProd_mean.csv 222 done < $outputDir/junctionAnalysisUnProd_mean.csv
222 echo "</tbody></table>" >> $outputFile 223 echo "</tbody></table>" >> $outputFile
223 224
224 echo "<table border='1' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile 225 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Productive median</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile
225 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP 226 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP
226 do 227 do
227 echo "<tr><td>$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></tr>" >> $outputFile 228 echo "<tr><td>$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></tr>" >> $outputFile
228 done < $outputDir/junctionAnalysisProd_median.csv 229 done < $outputDir/junctionAnalysisProd_median.csv
229 echo "</tbody></table>" >> $outputFile 230 echo "</tbody></table>" >> $outputFile
230 231
231 echo "<table border='1' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile 232 echo "<table class='pure-table pure-table-striped' id='junction_table'> <caption>Unproductive median</caption><thead><tr><th>Sample</th><th>count</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><thead></tr><tbody>" >> $outputFile
232 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP 233 while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP
233 do 234 do
234 echo "<tr><td>$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></tr>" >> $outputFile 235 echo "<tr><td>$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></tr>" >> $outputFile
235 done < $outputDir/junctionAnalysisUnProd_median.csv 236 done < $outputDir/junctionAnalysisUnProd_median.csv
236 echo "</tbody></table>" >> $outputFile 237 echo "</tbody></table>" >> $outputFile
247 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile 248 echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
248 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile 249 echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
249 echo "</div></div>" >> $outputFile 250 echo "</div></div>" >> $outputFile
250 251
251 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile 252 echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
252 echo "<table border='1'>" >> $outputFile 253 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
253 echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile 254 echo "<thead><tr><th>Description</th><th>Link</th></tr></thead>" >> $outputFile
254 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>Download</a></td></tr>" >> $outputFile 255 echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>Download</a></td></tr>" >> $outputFile
255 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile 256 echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.csv'>Download</a></td></tr>" >> $outputFile
256 257
257 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile 258 echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
258 259