Mercurial > repos > davidvanzessen > report_clonality_igg

comparison r_wrapper.sh @ 7:1d0ed31089c6 draft

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Uploaded
author davidvanzessen
date Tue, 25 Mar 2014 07:08:12 -0400
parents 18ac92a69ef1
children 712f3e9924d5
comparison
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6:18ac92a69ef1 7:1d0ed31089c6
77 echo "</table></div>" >> $outputFile 77 echo "</table></div>" >> $outputFile
78 done 78 done
79 echo "</div></div>" >> $outputFile 79 echo "</div></div>" >> $outputFile
80 fi 80 fi
81 81
82 if [[ "$hasReplicateColumn" == "Yes" ]] ; then 82 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
83
84 if [[ "$hasJunctionData" == "Yes" ]] ; then
83 echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table' class='tablesorter'><thead><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile 85 echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table' class='tablesorter'><thead><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th><thead></tr><tbody>" >> $outputFile
84 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP 86 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
85 do 87 do
86 echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile 88 echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
87 done < $outputDir/junctionAnalysis.csv 89 done < $outputDir/junctionAnalysis.csv