# HG changeset patch # User sblanck # Date 1589294436 14400 # Node ID 4d539083cf7f422784adbac7e0a935d7b4d77e43 planemo upload for repository https://github.com/sblanck/MPAgenomics4Galaxy/tree/master/mpagenomics_wrappers commit 689d0d8dc899a683ee18700ef385753559850233-dirty diff -r 000000000000 -r 4d539083cf7f extractCN.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extractCN.R Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,170 @@ +#!/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("--settings_type",type="character",default=NULL, dest="settings_type"), + make_option("--settings_tumor",type="character",default=NULL, dest="settings_tumor"), + make_option("--symmetrize",type="character",default=NULL, dest="symmetrize"), + make_option("--settings_signal",type="character",default=NULL, dest="settings_signal"), + make_option("--settings_snp",type="character",default=NULL, dest="settings_snp"), + 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") +); + +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 +input=opt$input +tmp_dir=opt$new_file_path +output=opt$output +settingsType=opt$settings_type +tumorcsv=opt$settings_tumor +symmetrize=opt$symmetrize +signal=opt$settings_signal +snp=type.convert(opt$settings_snp) +outputlog=opt$outputlog +log=opt$log +user=opt$userid + +library(MPAgenomics) +workdir=file.path(tmp_dir, "mpagenomics",user) +setwd(workdir) + +inputDataset=read.table(file=input,stringsAsFactors=FALSE) +dataset=inputDataset[1,2] + +if (outputlog){ + sinklog <- file(log, open = "wt") + sink(sinklog ,type = "output") + sink(sinklog, type = "message") +} + + +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 (settingsType == "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(settingsType,",") + 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 (settingsType == "dataset") { + input_vecstring = getListOfFiles(dataset) + } else { + input_tmp <- strsplit(settingsType,",") + 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 (settingsType == "dataset") { + if (tumorcsv== "None") + { + fracB=getFracBSignal(dataset,chromosome=chrom_vec) + + } else { + fracB=getFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv) + } + } else { + input_tmp <- strsplit(settingsType,",") + 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") + } + +} + +if (outputlog){ + sink(type="output") + sink(type="message") + close(sinklog) +} \ No newline at end of file diff -r 000000000000 -r 4d539083cf7f extractCN.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/extractCN.xml Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,222 @@ + + copy number or allele B fraction signal + mpagenomics + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + outputlog == "TRUE" + + + + + + +.. class:: warningmark + +Data normalization must be run (with the data normalization tool) prior to signal extraction. + +----- + +**What it does** +This tool extracts the copy number profile from the normalized data. + +Outputs: + +*A tabular text file containing 3 fixed columns and 1 column per sample:* + + - chr: Chromosome. + - position: Genomic position (in bp). + - probeNames: Name of the probes of the microarray. + - One column per sample which contains the copy number profile for each sample. + +----- + +**Normal-tumor study** + +In cases where normal (control) samples match to tumor samples, normalization can be improved using TumorBoost. In this case, a normal-tumor csv file must be provided : + + - The first column contains the names of the files corresponding to normal samples of the dataset. + + - The second column contains the names of the tumor samples files. + + - Column names of these two columns are respectively normal and tumor. + + - Columns are separated by a comma. + + - *Extensions of the files (.CEL for example) should be removed* + + + +**Example** + +Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel files.) :: + + patient1_normal.cel + patient1_tumor.cel + patient2_normal.cel + patient2_tumor.cel + patient3_normal.cel + patient3_tumor.cel + + +The csv file should look like this :: + + normal,tumor + patient1_normal,patient1_tumor + patient2_normal,patient2_tumor + patient3_normal,patient3_tumor + +----- + + +**Citation** + +If you use this tool please cite : + +`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. Mpagenomics : An r package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ + + + + diff -r 000000000000 -r 4d539083cf7f filter.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.R Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,67 @@ +#!/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("--length",type="character",default=NULL, dest="length"), + make_option("--probes",type="character",default=NULL, dest="probes"), + make_option("--outputlog",type="character",default=NULL, dest="outputlog"), + make_option("--log",type="character",default=NULL, dest="log") + ); + +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$new_file_path +nbcall=opt$nbcall +length=as.numeric(opt$length) +probes=as.numeric(opt$probes) +log=opt$log +outputlog=opt$outputlog + +if (outputlog){ + sinklog <- file(log, open = "wt") + sink(sinklog ,type = "output") + sink(sinklog, type = "message") +} + +nbcall_tmp <- strsplit(nbcall,",") +nbcall_vecstring <-unlist(nbcall_tmp) + +nbcall_vecstring + +library(MPAgenomics) +workdir=file.path(tmp_dir, "mpagenomics") +setwd(workdir) + +segcall = read.table(input, header = TRUE) +filtercall=filterSeg(segcall,length,probes,nbcall_vecstring) +#sink(output) +#print(format(filtercall),row.names=FALSE) +#sink() +if (outputlog){ + sink(type="output") + sink(type="message") + close(sinklog) +} +write.table(filtercall,output,row.names = FALSE, quote = FALSE, sep = "\t") + diff -r 000000000000 -r 4d539083cf7f filter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter.xml Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,74 @@ + + mpagenomics + + + + + + + + + + + + + + + + + + + + + + + + + outputlog == "TRUE" + + + + + + + + +**What it does** + +This tool filters results obtained by the segmentation and calling tool. + +----- + +Input/Output file: + +*A tabular text file containing 7 columns:* + + - sampleNames: Name of the file. + - chrom: Chromosome of the segment. + - chromStart: Starting position (in bp) of the segment. This position is not included in the segment. + - chromEnd: Ending position (in bp) of the segment. This position is included in the segment. + - probes: Number of probes in the segment. + - means: Mean of the segment. + - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”). + +----- + +**Citation** + +If you use this tool please cite : + +`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ + + + diff -r 000000000000 -r 4d539083cf7f preprocess.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/preprocess.R Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,158 @@ +#!/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("--summary",type="character",default=NULL, dest="summary"), + make_option("--dataSetName",type="character",default=NULL, dest="dataSetName"), + make_option("--new_file_path",type="character",default=NULL, dest="new_file_path"), + make_option("--inputcdffull_name",type="character",default=NULL, dest="inputcdffull_name"), + make_option("--inputufl_name",type="character",default=NULL, dest="inputufl_name"), + make_option("--inputugp_name",type="character",default=NULL, dest="inputugp_name"), + make_option("--inputacs_name",type="character",default=NULL, dest="inputacs_name"), + make_option("--inputcdffull",type="character",default=NULL, dest="inputcdffull"), + make_option("--inputufl",type="character",default=NULL, dest="inputufl"), + make_option("--inputugp",type="character",default=NULL, dest="inputugp"), + make_option("--inputacs",type="character",default=NULL, dest="inputacs"), + make_option("--tumorcsv",type="character",default=NULL, dest="tumorcsv"), + make_option("--settingsType",type="character",default=NULL, dest="settingsType"), + make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"), + make_option("--zipfigures",type="character",default=NULL, dest="zipfigures"), + 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="user_id"), + make_option("--input",type="character",default=NULL, dest="input") +); + +opt_parser = OptionParser(option_list=option_list); +opt = parse_args(opt_parser); + +if(is.null(opt$input)){ + print_help(opt_parser) + stop("input required.", call.=FALSE) +} + +#loading libraries + +summary=opt$summary +dataSetName=opt$dataSetName +newFilePath=opt$new_file_path +inputCDFName=opt$inputcdffull_name +inputUFLName=opt$inputufl_name +inputUGPName=opt$inputugp_name +inputACSName=opt$inputacs_name +inputCDF=opt$inputcdffull +inputUFL=opt$inputufl +inputUGP=opt$inputugp +inputACS=opt$inputacs +tumorcsv=opt$tumorcsv +settingsType=opt$settingsType +outputGraph=opt$outputgraph +zipfigures=opt$zipfigures +outputlog=opt$outputlog +log=opt$log +userId=opt$user_id + +destinationPath=file.path(newFilePath, userId, dataSetName) +mpagenomicsDir = file.path(newFilePath,"mpagenomics",userId) +dataDir = file.path(newFilePath, userId) +chipDir = file.path(newFilePath,"mpagenomics",userId,"annotationData","chipTypes") +createArchitecture=TRUE + +if (dir.exists(chipDir)) + system(paste0("rm -r ", chipDir)) + +if (!dir.exists(mpagenomicsDir)) + dir.create(mpagenomicsDir, showWarnings = TRUE, recursive = TRUE) + +if (!dir.exists(dataDir)) + dir.create(dataDir, showWarnings = TRUE, recursive = TRUE) + +listInput <- trimws( unlist( strsplit(trimws(opt$input), ",") ) ) +if(length(listInput)<2){ + stop("To few .CEL files selected : At least 2 .CEL files are required", call.=FALSE) +} + + +celList=vector() +celFileNameList=vector() + +for (i in 1:length(listInput)) +{ + inputFileInfo <- unlist( strsplit( listInput[i], ';' ) ) + celList=c(celList,inputFileInfo[1]) + celFileNameList=c(celFileNameList,inputFileInfo[2]) +} + + +for (i in 1:length(celFileNameList)) + { + source = celList[i] + destination=file.path(dataDir,celFileNameList[i]) + file.copy(source, destination) +} +split=unlist(strsplit(inputCDFName,",",fixed=TRUE)) +tag=NULL +if (length(split) != 0) { + chipType=split[1] + tagExt=split[2] + tag=unlist(strsplit(tagExt,".",fixed=TRUE))[1] + } else { + chipType=split[1] +} + +if(!file.exists(file.path(dataDir,inputCDFName))) + file.symlink(inputCDF,file.path(dataDir,inputCDFName)) +if(!file.exists(file.path(dataDir,inputACSName))) + file.symlink(inputACS,file.path(dataDir,inputACSName)) +if(!file.exists(file.path(dataDir,inputUFLName))) + file.symlink(inputUFL,file.path(dataDir,inputUFLName)) +if(!file.exists(file.path(dataDir,inputUGPName))) + file.symlink(inputUGP,file.path(dataDir,inputUGPName)) + +fig_dir = file.path("mpagenomics", userId, "figures", dataSetName, "signal") +abs_fig_dir = file.path(newFilePath, fig_dir) + +chip=chipType +dataset=dataSetName +workdir=mpagenomicsDir +celPath=dataDir +chipPath=dataDir +tumor=tumorcsv +outputgraph=type.convert(outputGraph) + + +library(MPAgenomics) +setwd(workdir) + +if (outputlog){ + sinklog <- file(log, open = "wt") + sink(sinklog ,type = "output") + sink(sinklog, type = "message") +} + +if (settingsType=="standard") +{ + signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, path=workdir,createArchitecture=createArchitecture, savePlot=outputgraph, tags=tag) +} else { + signalPreProcess(dataSetName=dataset, chipType=chip, dataSetPath=celPath,chipFilesPath=chipPath, normalTumorArray=tumor, path=workdir,createArchitecture=createArchitecture, savePlot=outputgraph, tags=tag) +} +setwd(abs_fig_dir) +files2zip <- dir(abs_fig_dir) +zip(zipfile = "figures.zip", files = files2zip) +file.rename("figures.zip",zipfigures) +summarydf=data.frame(celFileNameList,rep(dataSetName,length(celFileNameList)),rep(chipType,length(celFileNameList))) +write.table(summarydf,file=summary,quote=FALSE,row.names=FALSE,col.names=FALSE,sep="\t") + +if (outputlog){ + sink(type="output") + sink(type="message") + close(sinklog) +} + diff -r 000000000000 -r 4d539083cf7f preprocess.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/preprocess.xml Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,159 @@ + + + + mpagenomics + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + outputgraph == "TRUE" + + + outputlog == "TRUE" + + + + + + + + + +**What it does** + +This preprocessing step consists in a correction of biological and technical biaises due to the experiment. Raw data from Affymetrix arrays are provided in different CEL files. These data must be normalized before statistical analysis. +The pre-processing is proposed as a wrapper of aroma.* packages (using CRMAv2 and TumorBoost when appropriate). Note that this implies that the pre-processing step is only available for Affymetrix arrays. + +----- + +**Chip file naming conventions** + +Chip filenames must strictly follow the following rules : + +- *.cdf* filename must comply with the following format : < chiptype >,< tag >.cdf (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full.cdf). Note the use of a comma (not a point) between <chiptype> and the tag "Full". + +- *.ufl* filename must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl). + +- *.ugp* filename must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp). + +- *.acs* file name must start with < chiptype >,< tag > (e.g, for a GenomeWideSNP_6 chip: GenomeWideSNP_6,HB20080710.acs). + +----- + +**Normal-tumor study with TumorBoost** + +In cases where normal (control) samples match to tumor samples, normalization can be improved using TumorBoost. In this case, a normal-tumor csv file must be provided : + + - The first column contains the names of the files corresponding to normal samples of the dataset. + + - The second column contains the names of the tumor samples files. + + - Column names of these two columns are respectively normal and tumor. + + - Columns are separated by a comma. + + - *Extensions of the files (.CEL for example) should be removed* + + + +**Example** + +Let 6 .cel files in the dataset studied (3 patients, each of them being represented by a couple of normal and tumor cel files.) :: + + patient1_normal.cel + patient1_tumor.cel + patient2_normal.cel + patient2_tumor.cel + patient3_normal.cel + patient3_tumor.cel + + +The csv file should look like this :: + + normal,tumor + patient1_normal,patient1_tumor + patient2_normal,patient2_tumor + patient3_normal,patient3_tumor + + +----- + +**Citation** + +When using this tool, please cite : + +`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ + +As CRMAv2 normalization is used, please also cite `H. Bengtsson, P. Wirapati, and T. P. Speed. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics, 5(17):2149–2156, 2009. <http://bioinformatics.oxfordjournals.org/content/25/17/2149.short>`_ + +When using TumorBoost to improve normalization in a normal-tumor study, please cite `H. Bengtsson, P. Neuvial, and T. P. Speed. TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays. BMC Bioinformatics, 11, 2010 <http://www.biomedcentral.com/1471-2105/11/245>`_ + + + diff -r 000000000000 -r 4d539083cf7f repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,4 @@ + + + + \ No newline at end of file diff -r 000000000000 -r 4d539083cf7f segcall.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/segcall.R Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,124 @@ +#!/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") + diff -r 000000000000 -r 4d539083cf7f segcall.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/segcall.xml Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,212 @@ + + of the normalized data + mpagenomics + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + outputgraph == "TRUE" + + + outputlog == "TRUE" + + + + + + +.. class:: warningmark + +Data normalization must be run with the Data Normalization tool prior to segmentation. Otherwise, the standalone version can be used to perform marker selection from matrices containing data normalized with tools different from the one proposed in this instance. + + +----- + +**What it does** +This tool segments the previously normalized profiles and labels segments found in the copy-number profiles. Otherwise, the standalone version can be used to perform segmentation from matrices containing data normalized with tools different from the one proposed in this instance. + +Outputs: + +*A tabular text file containing 7 columns which describe all the segments (1 line per segment):* + + - sampleNames: Names of the original .CEL files. + - chrom: Chromosome of the segment. + - chromStart: Starting position (in bp) of the segment. This position is not included in the segment. + - chromEnd: Ending position (in bp) of the segment. This position is included in the segment. + - probes: Number of probes in the segment. + - means: Mean of the segment. + - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”). + +*A .zip file containing all the figures (optionnal)* + +----- + +**Normal-tumor study** + +In cases where normal (control) samples match to tumor samples, they are taken as references to extract copy number profile. In this case, a normal-tumor csv file must be provided : + + - The first column contains the names of the files corresponding to normal samples of the dataset. + + - The second column contains the names of the tumor samples files. + + - Column names of these two columns are respectively normal and tumor. + + - Columns are separated by a comma. + + - *Extensions of the files (.CEL for example) should be removed* + + + +**Example** + +Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel files.) :: + + patient1_normal.cel + patient1_tumor.cel + patient2_normal.cel + patient2_tumor.cel + patient3_normal.cel + patient3_tumor.cel + + +The csv file should look like this :: + + normal,tumor + patient1_normal,patient1_tumor + patient2_normal,patient2_tumor + patient3_normal,patient3_tumor + +----- + + +**Citation** + +If you use this tool please cite : + +`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ + +As segmentation is performed with PELT, please also cite `R. Killick, P. Fearnhead, and I. A. Eckley. Optimal detection of changepoints with a linear computational cost. Journal of the American Statistical Association, 107(500):1590–1598, 2012. <http://arxiv.org/abs/1101.1438>`_ + +As segmentation is performed by cghseg, please cite `Picard, F., Robin, S., Lavielle, M., Vaisse, C., and Daudin, J.-J. (2005). A statistical approach for array CGH data analysis. BMC Bioinformatics, 6(1):27. <http://www.ncbi.nlm.nih.gov/pubmed/15705208>`_ , +and also cite Rigaill, G. (2010). `Pruned dynamic programming for optimal multiple change-point detection. <http://arxiv.org/abs/1004.0887>`_ + +When using the labels of the segments, please cite CGHCall `M. A. van de Wiel, K. I. Kim, S. J. Vosse, W. N. van Wieringen, S. M. Wilting, and B. Ylstra. CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics, 23(7):892–894, 2007. <http://bioinformatics.oxfordjournals.org/content/23/7/892.abstract>`_ + + + diff -r 000000000000 -r 4d539083cf7f segmentFracB.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/segmentFracB.R Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,144 @@ +#!/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("--settings_type",type="character",default=NULL, dest="settingsType"), + make_option("--output_graph",type="character",default=NULL, dest="outputgraph"), + make_option("--zip_figures",type="character",default=NULL, dest="zipfigures"), + make_option("--settings_tumor",type="character",default=NULL, dest="settingsTypeTumor"), + 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 + +args<-commandArgs(TRUE) + +chrom=opt$chrom +datasetFile=opt$input +output=opt$output +tmp_dir=opt$new_file_path +input=opt$settingsType +outputfigures=type.convert(opt$outputgraph) +tumorcsv=opt$settingsTypeTumor +user=opt$userid +method=opt$method +log=opt$log +outputlog=opt$outputlog +outputgraph=opt$outputgraph +zipfigures=opt$zipfigures + +#chrom=opt$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] + + + +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) +} + +fig_dir = file.path("mpagenomics", user, "figures", dataset, "segmentation","fracB") +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 (input == 'dataset') { + segcall=segFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, savePlot=outputfigures, method=method) + +} else { + input_tmp <- strsplit(input,",") + input_tmp_vecstring <-unlist(input_tmp) + input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring) + segcall=segFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, savePlot=outputfigures, method=method) + +} +write.table(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) +} + +#sink(output) +#print(format(segcall)) +#sink() + + diff -r 000000000000 -r 4d539083cf7f segmentFracB.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/segmentFracB.xml Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,178 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + outputgraph == "TRUE" + + + outputlog == "TRUE" + + + + + + +.. class:: warningmark + +Data normalization must be run (with the data normalization tool) prior to segmentation. + +----- + +**What it does** +This tool segments allele B fraction extracted from the previously normalized data. This tools works only on normal-tumor study. + +Outputs: + +*A tabular text file containing 6 columns which describe all the segment (1 line per segment):* + + - sampleNames: Name of the file. + - chrom: The chromosome of the segment. + - chromStart: The starting position (in bp) of the segment. This position is not included in the segment. + - chromEnd: The ending position (in bp) of the segment. This position is included in the segment. + - probes: Number of probes in the segment. + - means: Mean of the segment. + +*A .zip file containing all the figures (optionnal)* + +----- + +**Normal-tumor csv files** + +Normal-tumor csv file is required to segment Allele B fraction, because naive genotyping is based on normal samples : + + - The first column contains the names of the files corresponding to normal samples of the dataset. + + - The second column contains the names of the tumor samples files. + + - Column names of these two columns are respectively normal and tumor. + + - Columns are separated by a comma. + + - *Extensions of the files (.CEL for example) should be removed* + + + +**Example** + +Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel files.) :: + + patient1_normal.cel + patient1_tumor.cel + patient2_normal.cel + patient2_tumor.cel + patient3_normal.cel + patient3_tumor.cel + + +The csv file should look like this :: + + normal,tumor + patient1_normal,patient1_tumor + patient2_normal,patient2_tumor + patient3_normal,patient3_tumor + +----- + + +**Citation** + +If you use this tool please cite : + +`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ + +If segmentation is performed with PELT, please cite `R. Killick, P. Fearnhead, and I. A. Eckley. Optimal detection of changepoints with a linear computational cost. Journal of the American Statistical Association, 107(500):1590–1598, 2012. <http://arxiv.org/abs/1101.1438>`_ + +If segmentation is performed by cghseg, please cite `Picard, F., Robin, S., Lavielle, M., Vaisse, C., and Daudin, J.-J. (2005). A statistical approach for array CGH data analysis. BMC Bioinformatics, 6(1):27. <http://www.ncbi.nlm.nih.gov/pubmed/15705208>`_ , +and also cite Rigaill, G. (2010). `Pruned dynamic programming for optimal multiple change-point detection. <http://arxiv.org/abs/1004.0887>`_ + + + \ No newline at end of file diff -r 000000000000 -r 4d539083cf7f segmentation.R --- /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) +} diff -r 000000000000 -r 4d539083cf7f segmentation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/segmentation.xml Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,114 @@ + + of a previously normalized signal + mpagenomics + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + outputlog == "TRUE" + + + outputgraph == "TRUE" + + + + + + + +**What it does** +This tool segments normalized profiles provided by the user and labels segments found in the copy-number profiles. + +Input format: + +*A tabular text file containing 3 fixed columns and 1 column per sample:* + + - chr: Chromosome. + - position: Genomic position (in bp) + - probeName: Probes names. + - One column per sample which contains the copy number profile for each sample + +Output format: + +*A tabular text file containing 7 columns which describe all the segments (1 line per segment):* + + - sampleNames: Column names corresponding to samples in the input file. + - chrom: Chromosome of the segment. + - chromStart: Starting position (in bp) of the segment. This position is not included in the segment. + - chromEnd: Ending position (in bp) of the segment. This position is included in the segment. + - probes: Number of probes in the segment. + - means: Mean of the segment. + - calls: Calling of the segment (”double loss”, ”loss”, ”normal”, ”gain” or ”amplification”). + +----- + +**Citation** +If you use this tool please cite : + +`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ + +If segmentation is performed with PELT, please also cite `R. Killick, P. Fearnhead, and I. A. Eckley. Optimal detection of changepoints with a linear computational cost. Journal of the American Statistical Association, 107(500):1590–1598, 2012. <http://arxiv.org/abs/1101.1438>`_ + +If segmentation is performed by cghseg, please cite `Picard, F., Robin, S., Lavielle, M., Vaisse, C., and Daudin, J.-J. (2005). A statistical approach for array CGH data analysis. BMC Bioinformatics, 6(1):27. <http://www.ncbi.nlm.nih.gov/pubmed/15705208>`_ , +and also cite Rigaill, G. (2010). `Pruned dynamic programming for optimal multiple change-point detection. <http://arxiv.org/abs/1004.0887>`_ + +When using the labels of the segments, please cite CGHCall `M. A. van de Wiel, K. I. Kim, S. J. Vosse, W. N. van Wieringen, S. M. Wilting, and B. Ylstra. CGHcall: calling aberrations for array CGH tumor profiles. Bioinformatics, 23(7):892–894, 2007. <http://bioinformatics.oxfordjournals.org/content/23/7/892.abstract>`_ + + + diff -r 000000000000 -r 4d539083cf7f selection.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/selection.R Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,135 @@ +#!/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("--response",type="character",default=NULL, dest="response"), + make_option("--settingsType",type="character",default=NULL, dest="settingsType"), + make_option("--outputgraph",type="character",default=NULL, dest="outputgraph"), + make_option("--settingsSnp",type="character",default=NULL, dest="settingsSnp"), + make_option("--settingsSignal",type="character",default=NULL, dest="settingsSignal"), + make_option("--settingsLoss",type="character",default=NULL, dest="settingsLoss"), + make_option("--pdffigures",type="character",default=NULL, dest="pdffigures"), + make_option("--folds",type="character",default=NULL, dest="folds"), + 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("--settingsPackage",type="character",default=NULL, dest="settingsPackage") +); + +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$chrom +dataset=opt$input +dataResponse=opt$response +output=opt$output +tmp_dir=opt$new_file_path +signal=opt$settingsSignal +settingsType=opt$settingsType +outputfigures=type.convert(opt$outputgraph) +snp=type.convert(opt$settingsSnp) +user=opt$userid +folds=as.numeric(opt$folds) +loss=opt$settingsLoss +log=opt$log +outputlog=opt$outputlog +outputgraph=opt$outputgraph +pdffigures=opt$pdffigures +package=opt$settingsPackage + + +library(MPAgenomics) +library(glmnet) +library(spikeslab) +library(lars) + +inputDataset=read.table(file=dataset,stringsAsFactors=FALSE) +input=inputDataset[1,2] +workdir=file.path(tmp_dir, "mpagenomics",user) +print(workdir) +setwd(workdir) + +if (grepl("all",tolower(chrom)) | chrom=="None") { + chrom_vec=c(1:25) + } else { + chrom_tmp <- strsplit(chrom,",") + chrom_vecstring <-unlist(chrom_tmp) + chrom_vec <- as.numeric(chrom_vecstring) + } + +if (outputlog){ + sinklog <- file(log, open = "wt") + sink(sinklog ,type = "output") + sink(sinklog, type = "message") +} + +if (settingsType == "tumor") { + if (signal=="CN") { + res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, normalTumorArray=tumor, onlySNP=snp, loss=loss, plot=outputfigures, nbFolds=folds, pkg=package) + } else { + res=markerSelection(input,dataResponse, chromosome=chrom_vec,signal=signal,normalTumorArray=tumor, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package) + } +} else { + if (signal=="CN") { + res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, onlySNP=snp, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package) + } else { + res=markerSelection(input,dataResponse, chromosome=chrom_vec, signal=signal, loss=loss, plot=outputfigures, nbFolds=folds,pkg=package) + } +} + +res + +df=data.frame() +list_chr=names(res) +markerSelected=FALSE + +for (i in list_chr) { + chr_data=res[[i]] + len=length(chr_data$markers.index) + if (len != 0) + { + markerSelected=TRUE + chrdf=data.frame(rep(i,len),chr_data$markers.position,chr_data$markers.index,chr_data$markers.names,chr_data$coefficient) + df=rbind(df,chrdf) + } +} + +if (outputgraph){ + file.rename(file.path(tmp_dir,"mpagenomics",user,"Rplots.pdf"), pdffigures) +} + +if (outputlog){ + sink(type="output") + sink(type="message") + close(sinklog) +} + +if (markerSelected) { + colnames(df) <- c("chr","position","index","names","coefficient") + #sink(output) + #print(format(df),row.names=FALSE) + #sink() + write.table(df,output,row.names = FALSE, quote = FALSE, sep = "\t") +} else + writeLines("no SNP selected", output) + + diff -r 000000000000 -r 4d539083cf7f selection.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/selection.xml Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,235 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + outputgraph == "TRUE" + (settingsLoss['package'] != 'spikeslab') + + + outputlog == "TRUE" + + + + + + +.. class:: warningmark + +Data normalization must be run with the Data Normalization tool prior to SNPs selection. Otherwise, the standalone version can be used to perform marker selection from matrices containing data normalized with tools different from the one proposed in this instance. + +----- + +**What it does** + +This tool selects some relevant markers according to a response using penalized regressions. + +Output: + +A tabular text file containing 5 columns which describe all the selected SNPs (1 line per SNPs): + + - chr: Chromosome containing the selected SNP. + - position: Position of the selected SNP. + - index: Index of the selected SNP. + - names: Name of the selected SNP. + - coefficient: Regression coefficient of the selected SNP. + +----- + +**Data Response csv file** + +Data response csv file format: + + - The first column contains the names of the different files of the data-set. + + - The second column contains the response associated with each file. + + - Column names of these two columns are respectively files and response. + + - Columns are separated by a comma + + - *Extensions of the files (.CEL for example) should be removed* + + + +**Example** + +Let 3 .cel files in the studied dataset :: + + patient1.cel + patient2.cel + patient3.cel + +The csv file should look like this :: + + files,response + patient1,1.92145 + patient2,2.12481 + patient3,1.23545 + + +----- + +**Normal-tumor study** + +In cases where normal (control) samples match to tumor samples, they are taken as references to extract copy number profile. In this case, a normal-tumor csv file must be provided : + + - The first column contains the names of the files corresponding to normal samples of the dataset. + + - The second column contains the names of the tumor samples files. + + - Column names of these two columns are respectively normal and tumor. + + - Columns are separated by a comma. + + - *Extensions of the files (.CEL for example) should be removed* + + +**Example** + +Let 6 .cel files in the studied dataset (3 patients, each of them being represented by a couple of normal and tumor cel file.) :: + + patient1_normal.cel + patient1_tumor.cel + patient2_normal.cel + patient2_tumor.cel + patient3_normal.cel + patient3_tumor.cel + + +The csv file should look like this :: + + normal,tumor + patient1_normal,patient1_tumor + patient2_normal,patient2_tumor + patient3_normal,patient3_tumor + +----- + + + +**Citation** + +If you use this tool please cite : + +`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ + + + diff -r 000000000000 -r 4d539083cf7f selectionExtracted.R --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/selectionExtracted.R Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,89 @@ +#!/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("--response",type="character",default=NULL, dest="response"), + make_option("--loss",type="character",default=NULL, dest="loss"), + make_option("--folds",type="character",default=NULL, dest="folds"), + make_option("--outputlog",type="character",default=NULL, dest="outputlog"), + make_option("--log",type="character",default=NULL, dest="log") +); + +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 +response=opt$response +output=opt$output +tmp_dir=opt$new_file_path +nbFolds=as.numeric(opt$folds) +loss=opt$loss +log=opt$log +outputlog=opt$outputlog + + +#args<-commandArgs(TRUE) +# +#input=args[1] +#response=args[2] +#tmp_dir=args[3] +#nbFolds=as.numeric(args[4]) +#loss=args[5] +#output=args[6] + +library(MPAgenomics) +workdir=file.path(tmp_dir, "mpagenomics") +setwd(workdir) + +if (outputlog){ + sinklog <- file(log, open = "wt") + sink(sinklog ,type = "output") + sink(sinklog, type = "message") +} + +CN=read.table(input,header=TRUE,check.names=FALSE) +drops=c("chromosome","position","probeName") +CNsignal=CN[,!(names(CN)%in% drops)] +samples=names(CNsignal) +CNsignalMatrix=t(data.matrix(CNsignal)) +resp=read.table(response,header=TRUE,sep=",") +listOfFile=resp[[1]] +responseValue=resp[[2]] +index = match(listOfFile,rownames(CNsignalMatrix)) +responseValueOrder=responseValue[index] + +result=variableSelection(CNsignalMatrix,responseValueOrder,nbFolds=nbFolds,loss=loss,plot=TRUE) + +CNsignalResult=CN[result$markers.index,(names(CN)%in% drops)] + +CNsignalResult["coefficient"]=result$coefficient +CNsignalResult["index"]=result$markers.index + +if (outputlog){ + sink(type="output") + sink(type="message") + close(sinklog) +} + +#sink(output) +#print(format(CNsignalResult),row.names=FALSE) +#sink() +write.table(CNsignalResult,output,row.names = FALSE, quote=FALSE, sep = "\t") diff -r 000000000000 -r 4d539083cf7f selectionExtracted.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/selectionExtracted.xml Tue May 12 10:40:36 2020 -0400 @@ -0,0 +1,111 @@ + + of previously extracted signal + + + + + + + + + + + + + + + + + + + + + + + + + outputlog == "TRUE" + + + + + + + **What it does** + +This tool selects some relevant markers according to a response using penalized regressions. + +Input: + +*A tabular text file containing 3 fixed columns and 1 column per sample:* + + - chr: Chromosome. + - position: Genomic position (in bp). + - probeNames: Names of the probes. + - One column per sample which contain the copy number signal for each sample. + +Output: + +*A tabular text file containing 5 columns which describe all the selected SNPs (1 line per SNP):* + + - chr: Chromosome containing the selected SNP. + - position: Position of the selected SNP. + - index: Index of the selected SNP. + - names: Name of the selected SNP. + - coefficient: Regression coefficient of the selected SNP. + +----- + +**Data Response csv file** + +Data response csv file format: + + - The first column contains the names of the different files of the dataset. + + - The second column is the response associated with each file. + + - Column names of these two columns are respectively files and response. + + - Columns are separated by a comma + + - *Extensions of the files (.CEL for example) should be removed* + + + +**Example** + +Let 3 .cel files in the studied dataset :: + + patient1.cel + patient2.cel + patient3.cel + +The csv file should look like this :: + + files,response + patient1,1.92145 + patient2,2.12481 + patient3,1.23545 + + +----- + +**Citation** + +If you use this tool please cite : + +`Q. Grimonprez, A. Celisse, M. Cheok, M. Figeac, and G. Marot. MPAgenomics : An R package for multi-patients analysis of genomic markers, 2014. Preprint <http://fr.arxiv.org/abs/1401.5035>`_ + + +