diff rdata_extractor.R @ 0:10212598b005 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rdata_extractor.R	Tue Aug 07 06:02:29 2018 -0400
@@ -0,0 +1,79 @@
+#!/usr/bin/env Rscript
+#Use a Rdata file and attributes to extract
+#Get every argument and write a file with its values(s)
+
+
+#get the rdata file
+args = commandArgs(trailingOnly=TRUE)
+rdata<-load(args[1])
+rdata<-get(rdata)
+sum<-summary(rdata) 
+
+#get the selected attributes to explore
+attributes_selected <- commandArgs(trailingOnly=TRUE)[2]
+attributes<-strsplit(attributes_selected, ",") #List of elements
+
+write.table(sum,file = "summary.tabular",sep='\t',row.names=FALSE)
+len<-length(attributes[[1]])-1
+bind<-tail(args,n=1)
+
+#file type definition
+file_ext<-function(ext){
+	file<-paste(attributes[[1]][i],ext,sep="") #Filename definition
+        file<-paste("outputs/",file,sep="")
+	return(file)
+}
+
+for (i in 1:len){
+	attribute<-attributes[[1]][i] #Get the attribute i 
+	if(! any(names(rdata)==attribute)){
+		error<-paste(attribute, " doesn't exist in the RData. Check the inputs files")
+		write(error, stderr())
+	}
+
+	attribute_val<-eval(parse(text=paste("rdata$",attribute,sep=""))) #Extract the value(s)
+
+	if(is.null(attribute_val)){ #Galaxy can't produce output if NULL
+		file<-file_ext(".txt")
+		write("Return NULL value",file=file)
+		next #Exit loop
+	}
+
+	if (typeof(attribute_val)=="list"){ #Need to be corrected, fail in galaxy but not in R
+		if(length(attribute_val)=="0"){
+			file<-file_ext(".txt")
+			sink(file=file)
+			print("Empty list :") #If the list is empty without element, file is empty and an error occur in galaxy
+			print(attribute_val)
+			sink()
+			next
+		}else{
+			attribute_val<-as.data.frame(do.call(rbind, attribute_val))
+			file<-file_ext(".tabular")
+			write.table(attribute_val,file=file,row.names=FALSE)
+			next
+		}
+	}else if (typeof(attribute_val)=="language"){ #OK
+		attribute_val<-toString(attribute_val,width = NULL)
+		file<-file_ext(".txt")
+		write(attribute_val,file=file)
+		next
+	}
+        file<-file_ext(".tabular")
+        dataframe<-as.data.frame(attribute_val)
+        names(dataframe)<-attribute
+        if(bind=="nobind"){
+            write.table(dataframe,file=file,row.names=FALSE,sep="    ")
+        }else{
+            if(!exists("alldataframe")){
+                alldataframe<-dataframe
+            }else{
+    	        alldataframe<-cbind(alldataframe, dataframe)
+            }
+        }
+}
+
+if(exists("alldataframe")&&bind=="bind"){
+    write.table(alldataframe,file=file,row.names=FALSE,sep="	")
+}
+q('no')