annotate segcall.R @ 0:4d539083cf7f draft

planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty

#!/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("--chrom",type="character",default=NULL, dest="chrom"),
		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("--settingsType",type="character",default=NULL, dest="settingsType"),
		make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"),
		make_option("--snp",type="character",default=NULL, dest="snp"),
		make_option("--zipfigures",type="character",default=NULL, dest="zipfigures"),
		make_option("--settingsTypeTumor",type="character",default=NULL, dest="settingsTypeTumor"),
		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("--userid",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

chrom=opt$chrom
datasetFile=opt$input
output=opt$output
tmp_dir=opt$new_file_path
nbcall=as.numeric(opt$nbcall)
settingsType=opt$settingsType
outputfigures=type.convert(opt$outputgraph)
snp=type.convert(opt$snp)
tumorcsv=opt$settingsTypeTumor
cellularity=as.numeric(opt$cellularity)
user=opt$userid
method=opt$method
log=opt$log
outputlog=opt$outputlog
outputgraph=opt$outputgraph
zipfigures=opt$zipfigures

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 (outputlog){
	sinklog <- file(log, open = "wt")
	sink(sinklog ,type = "output")
	sink(sinklog, type = "message")
} 
	
	
inputDataset=read.table(file=datasetFile,stringsAsFactors=FALSE)
dataset=inputDataset[1,2]

fig_dir = file.path("mpagenomics", user, "figures", dataset, "segmentation","CN")
abs_fig_dir = file.path(tmp_dir, fig_dir)

if (outputgraph) {
	if (dir.exists(abs_fig_dir)) {
		system(paste0("rm -r ", abs_fig_dir))
	}
}

if (settingsType == 'dataset') {
	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 {
	input_tmp <- strsplit(settingsType,",")
	input_tmp_vecstring <-unlist(input_tmp)
	input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) 
  	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)
  	}
}


write.table(format(segcall),output,row.names = FALSE, quote=FALSE, sep = "\t")


if (outputgraph) {	
	setwd(abs_fig_dir)
	files2zip <- dir(abs_fig_dir)
	zip(zipfile = "figures.zip", files = files2zip)
	file.rename("figures.zip",zipfigures)
}

if (outputlog){
	sink(type="output")
	sink(type="message")
	close(sinklog)
} 
#write.fwf(segcall,output,rownames = FALSE, quote=FALSE, sep = "\t")