diff segcall.R @ 5:b7f3854e08f8

Adding all tools

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segcall.R	Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,55 @@
+args<-commandArgs(TRUE)
+
+chrom=args[1]
+dataset=args[2]
+output=args[3]
+tmp_dir=args[4]
+nbcall=as.numeric(args[5])
+input=args[6]
+outputfigures=type.convert(args[7])
+snp=type.convert(args[8])
+tumorcsv=args[9]
+cellularity=as.numeric(args[10])
+user=args[11]
+method=args[12]
+
+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)
+	}
+
+input_tmp <- strsplit(input,",")
+input_tmp_vecstring <-unlist(input_tmp)
+
+
+input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) 
+
+if (dataset == input) {
+	if (tumorcsv== "none")
+	{
+  		segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, nclass=nbcall, savePlot=outputfigures,onlySNP=snp, cellularity=cellularity, method=method)
+  	} else {
+  		segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, nclass=nbcall, savePlot=outputfigures,onlySNP=snp, cellularity=cellularity, method=method)
+  	}
+} else {
+  	if (tumorcsv== "none") 
+  	{
+  		segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, listOfFiles=input_vecstring, nclass=nbcall, savePlot=outputfigures, onlySNP=snp, cellularity=cellularity, method=method)
+  	} else {
+  		segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, nclass=nbcall, savePlot=outputfigures, onlySNP=snp, cellularity=cellularity, method=method)
+  	}
+}
+
+sink(output)
+print(format(segcall))
+sink()
+#write.table(format(segcall),output,row.names = FALSE, quote=FALSE, sep = "\t")
+#write.fwf(segcall,output,rownames = FALSE, quote=FALSE, sep = "\t")
+quit()