changeset 36:fd55088e48d2 draft

Uploaded

--- a/experimental_design.xml	Fri Jan 22 08:45:29 2016 -0500
+++ b/experimental_design.xml	Fri Jan 22 10:22:24 2016 -0500
@@ -1,14 +1,14 @@
 <tool id="experimentaldesign_igg" name="ExperimentalDesign" version="1.0">
 	<description> </description>
-	<command interpreter="python">
-		experimental_design/experimental_design.py 
+	<command interpreter="bash">
+		experimental_design/experimental_design.sh 
 		#for $i, $f in enumerate($patients)
             "$f.id"
             #for $j, $g in enumerate($f.samples)
             	${g.sample}
             #end for
 		#end for
-		--output $out_file
+		$out_file
 	</command>
 	<inputs>
 		<repeat name="patients" title="Patient" min="1" default="1">

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/experimental_design/experimental_design.r	Fri Jan 22 10:22:24 2016 -0500
@@ -0,0 +1,38 @@
+args <- commandArgs(trailingOnly = TRUE)
+
+print(args)
+
+inputs = args[1:(length(args) - 1)]
+output = args[length(args)]
+
+current.id = ""
+counter = 1
+
+result = NULL
+
+for(current in inputs){
+	if(grepl("/", current)){ #its a path to a file
+		print(paste("Adding file", counter, "to", current.id))
+		dat = read.table(current, sep="\t", header=T, quote="", fill=T)
+		
+		#IMGT check
+		
+		dat$Sample = current.id
+		dat$Replicate = counter
+		
+		if(is.null(result)){
+			result = dat[NULL,]
+		}
+		
+		result = rbind(result, dat)
+		
+		counter = counter + 1
+		
+	} else { #its an ID of a patient
+		print(paste("New patient", current))
+		current.id = current
+		counter = 1
+	}
+}
+
+write.table(result, output, sep="\t", quote=F, row.names=F, col.names=T)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/experimental_design/experimental_design.sh	Fri Jan 22 10:22:24 2016 -0500
@@ -0,0 +1,4 @@
+
+dir="$(cd "$(dirname "$0")" && pwd)"
+
+Rscript --verbose $dir/experimental_design.r $@ 2>&1

--- a/report_clonality/RScript.r	Fri Jan 22 08:45:29 2016 -0500
+++ b/report_clonality/RScript.r	Fri Jan 22 10:22:24 2016 -0500
@@ -492,17 +492,17 @@
 	PRODF.sample = PRODF[PRODF$Sample == smpl,]
 	
 	fltr = PRODF.sample$Top.V.Gene == ""
-	if(sum(fltr) > 0){
+	if(any(fltr, na.rm=T)){
 	  PRODF.sample[fltr, "Top.V.Gene"] = "NA"
 	}
-
+	
 	fltr = PRODF.sample$Top.D.Gene == ""
-	if(sum(fltr) > 0){
+	if(any(fltr, na.rm=T)){
 	  PRODF.sample[fltr, "Top.D.Gene"] = "NA"
 	}
 
 	fltr = PRODF.sample$Top.J.Gene == ""
-	if(sum(fltr) > 0){
+	if(any(fltr, na.rm=T)){
 	  PRODF.sample[fltr, "Top.J.Gene"] = "NA"
 	}