--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/segmentation.R	Tue May 12 10:40:36 2020 -0400
@@ -0,0 +1,139 @@
+#!/usr/bin/env Rscript
+# setup R error handling to go to stderr
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+library("optparse")
+
+##### Read options
+option_list=list(
+		make_option("--input",type="character",default=NULL, dest="input"),
+		make_option("--output",type="character",default=NULL, dest="output"),
+		make_option("--new_file_path",type="character",default=NULL, dest="new_file_path"),
+		make_option("--nbcall",type="character",default=NULL, dest="nbcall"),
+		make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"),
+		make_option("--graph",type="character",default=NULL, dest="graph"),
+		make_option("--signalType",type="character",default=NULL, dest="signalType"),
+		make_option("--cellularity",type="character",default=NULL, dest="cellularity"),
+		make_option("--outputlog",type="character",default=NULL, dest="outputlog"),
+		make_option("--log",type="character",default=NULL, dest="log"),
+		make_option("--user_id",type="character",default=NULL, dest="userid"),
+		make_option("--method",type="character",default=NULL, dest="method")
+);
+
+opt_parser = OptionParser(option_list=option_list);
+opt = parse_args(opt_parser);
+
+if(is.null(opt$input)){
+	print_help(opt_parser)
+	stop("input required.", call.=FALSE)
+}
+
+#loading libraries
+
+input=opt$input
+output=opt$output
+tmp_dir=opt$new_file_path
+nbcall=as.numeric(opt$nbcall)
+outputgraph=type.convert(opt$outputgraph)
+cellularity=as.numeric(opt$cellularity)
+userId=opt$userid
+method=opt$method
+log=opt$log
+outputlog=opt$outputlog
+graph=opt$graph
+signalType=opt$signalType
+
+#args<-commandArgs(TRUE)
+#
+#input=args[1]
+#tmp_dir=args[2]
+#nbcall=as.numeric(args[3])
+#cellularity=as.numeric(args[4]) 
+#output=args[5]
+#method=args[6]
+#userId=args[7]
+#signalType=args[8]
+
+library(MPAgenomics)
+workdir=file.path(tmp_dir,"mpagenomics",userId)
+setwd(workdir)
+
+if (outputlog){
+	sinklog <- file(log, open = "wt")
+	sink(sinklog ,type = "output")
+	sink(sinklog, type = "message")
+} 
+
+CN=read.table(input,header=TRUE)
+uniqueChr=unique(CN$chromosome)
+drops=c("chromosome","position","probeName")
+CNsignal=CN[,!(names(CN)%in% drops),drop=FALSE]
+
+samples=names(CNsignal)
+
+if (signalType=="CN")
+{
+
+result=data.frame(sampleNames=character(0),chrom=character(0),chromStart=numeric(0),chromEnd=numeric(0),probes=numeric(0),means=numeric(0),calls=character(0),stringsAsFactors=FALSE)
+
+for (chr in uniqueChr)
+{
+currentSubset=subset(CN, chromosome==chr)
+currentPositions=currentSubset["position"]
+for (sample in samples) 
+  {
+    currentSignal=currentSubset[sample]
+	if (length(which(!is.na(unlist(currentSignal))))>1)
+	{
+		currentSeg=segmentation(signal=unlist(currentSignal),position=unlist(currentPositions),method=method)
+    	callobj= callingObject(copynumber=currentSeg$signal, segmented=currentSeg$segmented,chromosome=rep(chr,length(currentSeg$signal)), position=currentSeg$startPos,sampleNames=sample)
+	    currentCall=callingProcess(callobj,nclass=nbcall,cellularity=cellularity,verbose=TRUE)
+	    currentResult=currentCall$segment
+	    currentResult["sampleNames"]=c(rep(sample,length(currentCall$segment$chrom)))
+	    result=rbind(result,currentResult)
+	}
+  }
+}
+finalResult=data.frame(sampleNames=result["sampleNames"],chrom=result["chrom"],chromStart=result["chromStart"],chromEnd=result["chromEnd"],probes=result["probes"],means=result["means"],calls=result["calls"],stringsAsFactors=FALSE)
+
+write.table(finalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")
+} else {
+	result=data.frame(sampleNames=character(0),chrom=character(0),start=numeric(0),end=numeric(0),points=numeric(0),means=numeric(0),stringsAsFactors=FALSE)
+	
+	for (chr in uniqueChr)
+	{
+		cat(paste0("chromosome ",chr,"\n"))
+		currentSubset=subset(CN, chromosome==chr)
+		currentPositions=currentSubset["position"]
+		for (sample in samples) 
+		{
+			cat(paste0("  sample ",sample,"..."))
+			currentSignal=currentSubset[sample]
+			if (length(which(!is.na(unlist(currentSignal))))>1)
+			{
+				currentSeg=segmentation(signal=unlist(currentSignal),position=unlist(currentPositions),method=method)
+				currentResult=currentSeg$segment
+				currentResult["chrom"]=c(rep(chr,length(currentSeg$segment$means)))
+				currentResult["sampleNames"]=c(rep(sample,length(currentSeg$segment$means)))
+				result=rbind(result,currentResult)
+				
+			}
+			cat(paste0("OK\n"))
+		}
+	}
+	finalResult=data.frame(sampleNames=result["sampleNames"],chrom=result["chrom"],chromStart=result["start"],chromEnd=result["end"],probes=result["points"],means=result["means"],stringsAsFactors=FALSE)
+	write.table(finalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")
+}
+
+if (outputgraph){
+	file.rename(file.path(tmp_dir,"mpagenomics",userId,"Rplots.pdf"), graph)
+}
+
+if (outputlog){
+	sink(type="output")
+	sink(type="message")
+	close(sinklog)
+}