diff extractCN.R @ 5:b7f3854e08f8

Adding all tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractCN.R	Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,120 @@
+args<-commandArgs(TRUE)
+
+chrom=args[1]
+dataset=args[2]
+output=args[3]
+tmp_dir=args[4]
+input=args[5]
+tumorcsv=args[6]
+signal=args[7]
+snp=type.convert(args[8])
+user=args[9]
+symmetrize=args[10]
+
+library(MPAgenomics)
+workdir=file.path(tmp_dir, "mpagenomics",user)
+setwd(workdir)
+
+
+if (grepl("all",tolower(chrom)) | chrom=="None") {
+		chrom_vec=c(1:25)
+	} else {
+		chrom_tmp <- strsplit(chrom,",")
+		chrom_vecstring <-unlist(chrom_tmp)
+		chrom_vec <- as.numeric(chrom_vecstring)
+	}
+if (signal == "CN")
+{
+	if (input == "dataset") {
+		if (tumorcsv== "None")
+		{  		
+			CN=getCopyNumberSignal(dataset,chromosome=chrom_vec, onlySNP=snp)
+					
+	  	} else {
+	  		CN=getCopyNumberSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, onlySNP=snp)
+	  	}
+	} else {
+		input_tmp <- strsplit(input,",")
+		input_tmp_vecstring <-unlist(input_tmp)
+		input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) 
+	  	if (tumorcsv== "None") 
+	  	{
+	  		CN=getCopyNumberSignal(dataset,chromosome=chrom_vec, listOfFiles=input_vecstring, onlySNP=snp)
+	  	} else {
+	  		CN=getCopyNumberSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, onlySNP=snp )
+	  	}
+	}
+	
+	list_chr=names(CN)
+	CN_global=data.frame(check.names = FALSE)
+	for (i in list_chr) {
+	  chr_data=data.frame(CN[[i]],check.names = FALSE)
+	  CN_global=rbind(CN_global,chr_data)
+	}
+	names(CN_global)[names(CN_global)=="featureNames"] <- "probeName"
+	write.table(format(CN_global), output, row.names = FALSE, quote = FALSE, sep = "\t")
+	
+} else {
+	if (symmetrize=="TRUE")	{
+		if (input == "dataset") {
+			input_vecstring = getListOfFiles(dataset)
+		} else {
+			input_tmp <- strsplit(input,",")
+			input_tmp_vecstring <-unlist(input_tmp)
+			input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) 
+		}
+		
+		symFracB_global=data.frame(check.names = FALSE)
+		
+		for (currentFile in input_vecstring) {
+			cat(paste0("extracting signal from ",currentFile,".\n"))
+			currentSymFracB=data.frame()
+			symFracB=getSymFracBSignal(dataset,chromosome=chrom_vec,file=currentFile,normalTumorArray=tumorcsv)
+			list_chr=names(symFracB)
+			for (i in list_chr) {
+				cat(paste0("   extracting ",i,".\n"))
+				chr_data=data.frame(symFracB[[i]]$tumor,check.names = FALSE)
+				currentSymFracB=rbind(currentSymFracB,chr_data)
+				
+			}
+			if (is.null(symFracB_global) || nrow(symFracB_global)==0) {
+				symFracB_global=currentSymFracB
+			} else {
+				symFracB_global=cbind(symFracB_global,currentFile=currentSymFracB[[3]])
+			}
+		}
+		names(symFracB_global)[names(symFracB_global)=="featureNames"] <- "probeName"
+		
+		write.table(format(symFracB_global), output, row.names = FALSE, quote = FALSE, sep = "\t")
+	} else {
+		if (input == "dataset") {
+			if (tumorcsv== "None")
+			{  		
+				fracB=getFracBSignal(dataset,chromosome=chrom_vec)
+				
+			} else {
+				fracB=getFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv)
+			}
+		} else {
+			input_tmp <- strsplit(input,",")
+			input_tmp_vecstring <-unlist(input_tmp)
+			input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) 
+			if (tumorcsv== "None") 
+			{
+				fracB=getFracBSignal(dataset,chromosome=chrom_vec, listOfFiles=input_vecstring)
+			} else {
+				fracB=getFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring)
+			}
+		}
+		#formatage des données
+		list_chr=names(fracB)
+		fracB_global=data.frame(check.names = FALSE)
+		for (i in list_chr) {
+			chr_data=data.frame(fracB[[i]]$tumor,check.names = FALSE)
+			fracB_global=rbind(fracB_global,chr_data)
+		}
+		names(fracB_global)[names(fracB_global)=="featureNames"] <- "probeName"
+		write.table(format(fracB_global), output, row.names = FALSE, quote = FALSE, sep = "\t")
+	}
+	
+}
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