Mercurial > repos > sblanck > mpagenomics
view segmentation.R @ 3:94fc6ed13946 draft
planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 7679c75b4a95df45311603e2dceda55b159ffb4b-dirty
author | sblanck |
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date | Tue, 16 Jun 2020 04:34:09 -0400 |
parents | 4d539083cf7f |
children | 3fcbb8030fcc |
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#!/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) }