Mercurial > repos > davidvanzessen > argalaxy_tools

changeset 16:cf1def1aaa74 draft

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Uploaded
author davidvanzessen
date Fri, 06 Nov 2015 05:12:17 -0500
parents 6e068ef43336
children ee1bda8c27c8
files complete.sh igblast/test.txt report_clonality/RScript.r
diffstat 3 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/complete.sh	Fri Aug 07 08:42:58 2015 -0400
+++ b/complete.sh	Fri Nov 06 05:12:17 2015 -0500
@@ -52,7 +52,8 @@
 	mergerInput+=($parsedFileName)
 	count=$((count+1))
 done
-wait
+
+echo "<tr><td>after loooop</td></tr>" >> $html
 
 echo "after loop"
 
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igblast/test.txt	Fri Nov 06 05:12:17 2015 -0500
@@ -0,0 +1,1 @@
+test1	test2	test3
--- a/report_clonality/RScript.r	Fri Aug 07 08:42:58 2015 -0400
+++ b/report_clonality/RScript.r	Fri Nov 06 05:12:17 2015 -0500
@@ -563,10 +563,6 @@
 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(.SD$X3V.REGION.trimmed.nt.nb, na.rm=T),
                                                P1=mean(.SD$P3V.nt.nb, na.rm=T),
@@ -591,6 +587,8 @@
                                                            mean(.SD$P3D.nt.nb, na.rm=T) +
                                                            mean(.SD$P5J.nt.nb, na.rm=T))),
                                          by=c("Sample")])
+  print(newData)
+  newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)
   write.table(newData, "junctionAnalysisProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
   
   newData = data.frame(data.table(UNPROD)[,list(unique=.N, 
@@ -617,6 +615,7 @@
 																													mean(.SD$P3D.nt.nb, na.rm=T) +
 																													mean(.SD$P5J.nt.nb, na.rm=T))),
                                           by=c("Sample")])
+  newData[,sapply(newData, is.numeric)] = round(newData[,sapply(newData, is.numeric)],1)
   write.table(newData, "junctionAnalysisUnProd.csv" , sep=",",quote=F,na="-",row.names=F,col.names=F)
 }