Report on:" >> $outputFile mkdir $outputDir/circos @@ -206,31 +205,31 @@ #if [[ "$hasJunctionData" == "Yes" ]] ; then if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Productive mean</caption><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 - while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + 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>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do - echo "<tr><td>$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>" >> $outputFile + echo "<tr><td>$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 done < $outputDir/junctionAnalysisProd_mean.csv echo "</tbody></table>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Unproductive mean</caption><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 - while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + 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>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do - echo "<tr><td>$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>" >> $outputFile + echo "<tr><td>$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 done < $outputDir/junctionAnalysisUnProd_mean.csv echo "</tbody></table>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Productive median</caption><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 - while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + 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>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do - echo "<tr><td>$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>" >> $outputFile + echo "<tr><td>$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 done < $outputDir/junctionAnalysisProd_median.csv echo "</tbody></table>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Unproductive median</caption><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 - while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + 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>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do - echo "<tr><td>$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>" >> $outputFile + echo "<tr><td>$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 done < $outputDir/junctionAnalysisUnProd_median.csv echo "</tbody></table>" >> $outputFile

# HG changeset patch # User davidvanzessen # Date 1470143144 14400 # Node ID 85a1d832d19733f7df0db65c0b44e574c4d4930a # Parent 69a6bba9ada9ccc8bf3a10ae3dcc154079408358 Uploaded diff -r 69a6bba9ada9 -r 85a1d832d197 report_clonality/r_wrapper.sh --- a/report_clonality/r_wrapper.sh Thu Jul 21 03:56:52 2016 -0400 +++ b/report_clonality/r_wrapper.sh Tue Aug 02 09:05:44 2016 -0400 @@ -47,7 +47,6 @@ done < $outputDir/productive_counting.txt echo "" >> $2 -echo "productive_counting.txt" echo "Report on:" >> $outputFile mkdir $outputDir/circos @@ -206,31 +205,31 @@ #if [[ "$hasJunctionData" == "Yes" ]] ; then if [ -a "$outputDir/junctionAnalysisProd_mean.csv" ] ; then echo "<div class='tabbertab' title='Junction Analysis'>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Productive mean</caption><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 - while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + 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>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do - echo "<tr><td>$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>" >> $outputFile + echo "<tr><td>$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 done < $outputDir/junctionAnalysisProd_mean.csv echo "</tbody></table>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Unproductive mean</caption><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 - while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + 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>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do - echo "<tr><td>$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>" >> $outputFile + echo "<tr><td>$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 done < $outputDir/junctionAnalysisUnProd_mean.csv echo "</tbody></table>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Productive median</caption><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 - while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + 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>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do - echo "<tr><td>$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>" >> $outputFile + echo "<tr><td>$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 done < $outputDir/junctionAnalysisProd_median.csv echo "</tbody></table>" >> $outputFile - echo "<table border='1' id='junction_table'> <caption>Unproductive median</caption><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 - while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP + 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>" >> $outputFile + while IFS=, read Sample unique VDEL P1 N1 P2 DELD DDEL P3 N2 P4 DELJ TotalDel TotalN TotalP do - echo "<tr><td>$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>" >> $outputFile + echo "<tr><td>$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 done < $outputDir/junctionAnalysisUnProd_median.csv echo "</tbody></table>" >> $outputFile