Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg
comparison r_wrapper.sh @ 8:043fd6613fd9 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 12 Jan 2015 04:32:40 -0500 |
| parents | a9053212a462 |
| children | 7dbc9ebcefce |
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| 7:a9053212a462 | 8:043fd6613fd9 |
|---|---|
| 110 fi | 110 fi |
| 111 | 111 |
| 112 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" | 112 hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" |
| 113 | 113 |
| 114 if [[ "$hasJunctionData" == "Yes" ]] ; then | 114 if [[ "$hasJunctionData" == "Yes" ]] ; then |
| 115 echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table'><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 | 115 echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table'><thead><tr><th>Sample</th><th>count</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>" >> $outputFile |
| 116 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP | 116 while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP |
| 117 do | 117 do |
| 118 echo "<tr><td>$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>" >> $outputFile | 118 echo "<tr><td>$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 |
| 119 done < $outputDir/junctionAnalysis.csv | 119 done < $outputDir/junctionAnalysis.csv |
| 120 echo "</tbody></table></div>" >> $outputFile | 120 echo "</tbody></table></div>" >> $outputFile |