Mercurial > repos > davidvanzessen > argalaxy_tools
changeset 10:edbf4fba5fc7 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 31 Jul 2015 08:08:05 -0400 |
| parents | 079eed22fdb6 |
| children | 0510cf1f7cbc |
| files | complete.sh report_clonality/RScript.r |
| diffstat | 2 files changed, 49 insertions(+), 44 deletions(-) [+] |
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--- a/complete.sh Thu Jul 30 10:00:08 2015 -0400 +++ b/complete.sh Fri Jul 31 08:08:05 2015 -0400 @@ -35,8 +35,8 @@ fi echo "working on $current" fileName=$(basename $current) - parsedFileName="${fileName%.*}" - parsedFileName="$PWD/$parsedFileName.parsed" + fileName="${fileName%.*}" + parsedFileName="$PWD/$fileName.parsed" f=$(file $current) zipType="Zip archive" zxType="XZ compressed data" @@ -44,7 +44,7 @@ then echo "<tr><td>Sample $count of patient $id is an archive file, using IMGT Loader</td></tr>" >> $html fileName=$(basename $current) - bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName $count $parsedFileName "tmp" + bash ${dir}/imgt_loader/imgt_loader.sh $current $parsedFileName "${fileName}" else echo "<tr><td>Sample $count of patient $id is not a zip file, using igBLASTn</td></tr>" >> $html #blastAndParse $current $id $count $fileName $parsedFileName &
--- a/report_clonality/RScript.r Thu Jul 30 10:00:08 2015 -0400 +++ b/report_clonality/RScript.r Fri Jul 31 08:08:05 2015 -0400 @@ -101,7 +101,8 @@ #write the complete dataset that is left over, will be the input if 'none' for clonaltype and 'no' for filterproductive -write.table(PRODF, "allUnique.csv", sep=",",quote=F,row.names=F,col.names=T) +write.table(PRODF, "allUnique.txt", sep=",",quote=F,row.names=F,col.names=T) +write.table(PRODF, "allUnique.csv", sep="\t",quote=F,row.names=F,col.names=T) write.table(UNPROD, "allUnproductive.csv", sep=",",quote=F,row.names=F,col.names=T) #write the samples to a file @@ -554,55 +555,59 @@ imgtcolumns = c("X3V.REGION.trimmed.nt.nb","P3V.nt.nb", "N1.REGION.nt.nb", "P5D.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "P3D.nt.nb", "N2.REGION.nt.nb", "P5J.nt.nb", "X5J.REGION.trimmed.nt.nb", "X3V.REGION.trimmed.nt.nb", "X5D.REGION.trimmed.nt.nb", "X3D.REGION.trimmed.nt.nb", "X5J.REGION.trimmed.nt.nb", "N1.REGION.nt.nb", "N2.REGION.nt.nb", "P3V.nt.nb", "P5D.nt.nb", "P3D.nt.nb", "P5J.nt.nb") if(all(imgtcolumns %in% colnames(inputdata))) { + print("MEAN P3V.nt.nb:") + print(PRODF$P3V.nt.nb) + print(mean(PRODF$P3V.nt.nb, na.rm=T)) + print(head(PRODF)) newData = data.frame(data.table(PRODF)[,list(unique=.N, - VH.DEL=mean(X3V.REGION.trimmed.nt.nb, na.rm=T), - P1=mean(P3V.nt.nb, na.rm=T), - N1=mean(N1.REGION.nt.nb, na.rm=T), - P2=mean(P5D.nt.nb, na.rm=T), - DEL.DH=mean(X5D.REGION.trimmed.nt.nb, na.rm=T), - DH.DEL=mean(X3D.REGION.trimmed.nt.nb, na.rm=T), - P3=mean(P3D.nt.nb, na.rm=T), - N2=mean(N2.REGION.nt.nb, na.rm=T), - P4=mean(P5J.nt.nb, na.rm=T), - DEL.JH=mean(X5J.REGION.trimmed.nt.nb, na.rm=T), - Total.Del=( mean(X3V.REGION.trimmed.nt.nb, na.rm=T) + - mean(X5D.REGION.trimmed.nt.nb, na.rm=T) + - mean(X3D.REGION.trimmed.nt.nb, na.rm=T) + - mean(X5J.REGION.trimmed.nt.nb, na.rm=T)), + VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), + P1=mean(.SD$P3V.nt.nb, na.rm=T), + N1=mean(.SD$N1.REGION.nt.nb, na.rm=T), + P2=mean(.SD$P5D.nt.nb, na.rm=T), + DEL.DH=mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T), + DH.DEL=mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T), + P3=mean(.SD$P3D.nt.nb, na.rm=T), + N2=mean(.SD$N2.REGION.nt.nb, na.rm=T), + P4=mean(.SD$P5J.nt.nb, na.rm=T), + DEL.JH=mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), + Total.Del=( mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T) + + mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T) + + mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T) + + mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T)), - Total.N=( mean(N1.REGION.nt.nb, na.rm=T) + - mean(N2.REGION.nt.nb, na.rm=T)), + Total.N=( mean(.SD$N1.REGION.nt.nb, na.rm=T) + + mean(.SD$N2.REGION.nt.nb, na.rm=T)), - Total.P=( mean(P3V.nt.nb, na.rm=T) + - mean(P5D.nt.nb, na.rm=T) + - mean(P3D.nt.nb, na.rm=T) + - mean(P5J.nt.nb, na.rm=T))), + Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) + + mean(.SD$P5D.nt.nb, na.rm=T) + + mean(.SD$P3D.nt.nb, na.rm=T) + + mean(.SD$P5J.nt.nb, na.rm=T))), by=c("Sample")]) write.table(newData, "junctionAnalysisProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) newData = data.frame(data.table(UNPROD)[,list(unique=.N, - VH.DEL=mean(X3V.REGION.trimmed.nt.nb, na.rm=T), - P1=mean(P3V.nt.nb, na.rm=T), - N1=mean(N1.REGION.nt.nb, na.rm=T), - P2=mean(P5D.nt.nb, na.rm=T), - DEL.DH=mean(X5D.REGION.trimmed.nt.nb, na.rm=T), - DH.DEL=mean(X3D.REGION.trimmed.nt.nb, na.rm=T), - P3=mean(P3D.nt.nb, na.rm=T), - N2=mean(N2.REGION.nt.nb, na.rm=T), - P4=mean(P5J.nt.nb, na.rm=T), - DEL.JH=mean(X5J.REGION.trimmed.nt.nb, na.rm=T), - Total.Del=( mean(X3V.REGION.trimmed.nt.nb, na.rm=T) + - mean(X5D.REGION.trimmed.nt.nb, na.rm=T) + - mean(X3D.REGION.trimmed.nt.nb, na.rm=T) + - mean(X5J.REGION.trimmed.nt.nb, na.rm=T)), + VH.DEL=mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T), + P1=mean(.SD$P3V.nt.nb, na.rm=T), + N1=mean(.SD$N1.REGION.nt.nb, na.rm=T), + P2=mean(.SD$P5D.nt.nb, na.rm=T), + DEL.DH=mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T), + DH.DEL=mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T), + P3=mean(.SD$P3D.nt.nb, na.rm=T), + N2=mean(.SD$N2.REGION.nt.nb, na.rm=T), + P4=mean(.SD$P5J.nt.nb, na.rm=T), + DEL.JH=mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T), + Total.Del=( mean(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T) + + mean(.SD$X5D.REGION.trimmed.nt.nb, na.rm=T) + + mean(.SD$X3D.REGION.trimmed.nt.nb, na.rm=T) + + mean(.SD$X5J.REGION.trimmed.nt.nb, na.rm=T)), - Total.N=( mean(N1.REGION.nt.nb, na.rm=T) + - mean(N2.REGION.nt.nb, na.rm=T)), + Total.N=( mean(.SD$N1.REGION.nt.nb, na.rm=T) + + mean(.SD$N2.REGION.nt.nb, na.rm=T)), - Total.P=( mean(P3V.nt.nb, na.rm=T) + - mean(P5D.nt.nb, na.rm=T) + - mean(P3D.nt.nb, na.rm=T) + - mean(P5J.nt.nb, na.rm=T))), + Total.P=( mean(.SD$P3V.nt.nb, na.rm=T) + + mean(.SD$P5D.nt.nb, na.rm=T) + + mean(.SD$P3D.nt.nb, na.rm=T) + + mean(.SD$P5J.nt.nb, na.rm=T))), by=c("Sample")]) write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F) }