Mercurial > repos > davidvanzessen > complete_immunerepertoire_igg
changeset 8:043fd6613fd9 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 12 Jan 2015 04:32:40 -0500 |
| parents | a9053212a462 |
| children | 7dbc9ebcefce |
| files | RScript.r r_wrapper.sh |
| diffstat | 2 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/RScript.r Mon Jan 05 09:30:08 2015 -0500 +++ b/RScript.r Mon Jan 12 04:32:40 2015 -0500 @@ -552,7 +552,7 @@ imgtcolumns = c("X3V.REGION.trimmed.nt.nb","P3V.nt.nb", "N1.REGION.nt.nb", "P5D.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "P3D.nt.nb", "N2.REGION.nt.nb", "P5J.nt.nb", "X5J.REGION.trimmed.nt.nb", "X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb") if(all(imgtcolumns %in% colnames(inputdata))) { - newData = data.frame(data.table(inputdata)[,list(unique=.N, + newData = data.frame(data.table(PRODF)[,list(unique=.N, VH.DEL=mean(X3V.REGION.trimmed.nt.nb, na.rm=T), P1=mean(P3V.nt.nb, na.rm=T), N1=mean(N1.REGION.nt.nb, na.rm=T),
--- a/r_wrapper.sh Mon Jan 05 09:30:08 2015 -0500 +++ b/r_wrapper.sh Mon Jan 12 04:32:40 2015 -0500 @@ -112,7 +112,7 @@ hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)" if [[ "$hasJunctionData" == "Yes" ]] ; then - 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 + 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>" >> $outputFile while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP do echo "<tr><td>$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