# HG changeset patch
# User blanck
# Date 1430294141 -7200
# Node ID b7f3854e08f8bcc642db02aac1985c676ffbf73a
# Parent 2b882515e1a3c1685ad740e49b2ca404522e5679
Adding all tools
diff -r 2b882515e1a3 -r b7f3854e08f8 extractCN.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/extractCN.R Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,120 @@
+args<-commandArgs(TRUE)
+
+chrom=args[1]
+dataset=args[2]
+output=args[3]
+tmp_dir=args[4]
+input=args[5]
+tumorcsv=args[6]
+signal=args[7]
+snp=type.convert(args[8])
+user=args[9]
+symmetrize=args[10]
+
+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 (signal == "CN")
+{
+ if (input == "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(input,",")
+ 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 (input == "dataset") {
+ input_vecstring = getListOfFiles(dataset)
+ } else {
+ input_tmp <- strsplit(input,",")
+ 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]]$tumor,check.names = FALSE)
+ currentSymFracB=rbind(currentSymFracB,chr_data)
+
+ }
+ if (is.null(symFracB_global) || nrow(symFracB_global)==0) {
+ symFracB_global=currentSymFracB
+ } else {
+ symFracB_global=cbind(symFracB_global,currentFile=currentSymFracB[[3]])
+ }
+ }
+ names(symFracB_global)[names(symFracB_global)=="featureNames"] <- "probeName"
+
+ write.table(format(symFracB_global), output, row.names = FALSE, quote = FALSE, sep = "\t")
+ } else {
+ if (input == "dataset") {
+ if (tumorcsv== "None")
+ {
+ fracB=getFracBSignal(dataset,chromosome=chrom_vec)
+
+ } else {
+ fracB=getFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv)
+ }
+ } else {
+ input_tmp <- strsplit(input,",")
+ input_tmp_vecstring <-unlist(input_tmp)
+ input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring)
+ if (tumorcsv== "None")
+ {
+ fracB=getFracBSignal(dataset,chromosome=chrom_vec, listOfFiles=input_vecstring)
+ } else {
+ fracB=getFracBSignal(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring)
+ }
+ }
+ #formatage des données
+ list_chr=names(fracB)
+ fracB_global=data.frame(check.names = FALSE)
+ for (i in list_chr) {
+ chr_data=data.frame(fracB[[i]]$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")
+ }
+
+}
\ No newline at end of file
diff -r 2b882515e1a3 -r b7f3854e08f8 extractCN.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/extractCN.py Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,78 @@
+import os
+import sys
+import subprocess
+import getopt
+
+def main(argv):
+
+ symmetrize="False"
+
+ try:
+ opts, args = getopt.getopt(argv,"hc:i:o:f:s:y:t:p:l:g:n:u:",["chrom=","input=","output=","new_file_path=","settings_type=","settings_tumor=","symmetrize=","outputlog=","log=","settings_signal=","settings_snp=","userid="])
+ except getopt.GetoptError as err:
+ print str(err)
+ sys.exit(2)
+ for opt, arg in opts:
+ if opt == '-h':
+ print 'extractCN.py'
+ sys.exit()
+ elif opt in ("-c", "--chrom"):
+ chromosome = arg
+ elif opt in ("-i", "--input"):
+ input_file = arg
+ elif opt in ("-o", "--output"):
+ output_file = arg
+ elif opt in ("-f", "--new_file_path"):
+ tmp_dir = arg
+ elif opt in ("-s", "--settings_type"):
+ input_type = arg
+ elif opt in ("-t", "--settings_tumor"):
+ settings_tumor = arg
+ elif opt in ("-y", "--symmetrize"):
+ symmetrize = arg
+ elif opt in ("-p", "--outputlog"):
+ outputlog = arg
+ elif opt in ("-l", "--log"):
+ log = arg
+ elif opt in ("-g", "--settings_signal"):
+ signal = arg
+ elif opt in ("-n", "--settings_snp"):
+ snp = arg
+ elif opt in ("-u", "--userid"):
+ user_id = arg
+
+
+
+ #===========================================================================
+ #chromosome=sys.argv[1]
+ #input_file=sys.argv[2]
+ # output_file=sys.argv[3]
+ # tmp_dir=sys.argv[4]
+ # input_type=sys.argv[5]
+ # settings_tumor=sys.argv[6]
+ # outputlog=sys.argv[7]
+ # log=sys.argv[8]
+ # signal=sys.argv[9]
+ # snp=sys.argv[10]
+ # user_id=sys.argv[11]
+ #===========================================================================
+ script_dir=os.path.dirname(os.path.abspath(__file__))
+
+ iFile=open(input_file,'r')
+ dataSetLine=iFile.readline()
+ dataset=dataSetLine.split("\t")[1]
+ iFile.close()
+
+ if (outputlog=="TRUE"):
+ errfile=open(log,'w')
+ else:
+ errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
+
+ retcode=subprocess.call(["Rscript", os.path.join(script_dir,"extractCN.R"), chromosome, dataset, output_file, tmp_dir, input_type, settings_tumor, signal,snp,user_id, symmetrize], stdout = errfile, stderr = errfile)
+
+ errfile.close()
+
+ sys.exit(retcode)
+
+if __name__ == "__main__":
+ main(main(sys.argv[1:]))
diff -r 2b882515e1a3 -r b7f3854e08f8 extractCN.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/extractCN.xml Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,219 @@
+
diff -r 2b882515e1a3 -r b7f3854e08f8 filter.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.R Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,25 @@
+args<-commandArgs(TRUE)
+
+input=args[1]
+length=as.numeric(args[2])
+probes=as.numeric(args[3])
+tmp_dir=args[4]
+nbcall=as.vector(args[5])
+output=args[6]
+
+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()
+#write.table(filtercall,output,row.names = FALSE, quote = FALSE, sep = "\t")
+
diff -r 2b882515e1a3 -r b7f3854e08f8 filter.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.py Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,23 @@
+import os
+import sys
+import subprocess
+
+def main():
+
+ tmp_dir=sys.argv[4]
+ outputlog=sys.argv[7]
+ log=sys.argv[8]
+ script_dir=os.path.dirname(os.path.abspath(__file__))
+
+ if (outputlog=="TRUE"):
+ errfile=open(log,'w')
+ else:
+ errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
+
+
+ retcode=(subprocess.call(["Rscript", os.path.join(script_dir,"filter.R"), sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4], sys.argv[5], sys.argv[6]], stdout = errfile, stderr = errfile))
+ errfile.close();
+ sys.exit(retcode)
+
+if __name__ == "__main__":
+ main()
\ No newline at end of file
diff -r 2b882515e1a3 -r b7f3854e08f8 filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/filter.xml Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,63 @@
+
+ mpagenomics
+
+ filter.py '$input' '$length' '$probes' '$__new_file_path__' '$nbcall' '$output' '$outputlog' '$log'
+
+
+
+
+
+
+
+
+
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+
+
+
+
+
+
+
+
+
+
+ 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 2b882515e1a3 -r b7f3854e08f8 markersSelection.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/markersSelection.R Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,35 @@
+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)
+
+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
+
+sink(output)
+print(format(CNsignalResult),row.names=FALSE)
+sink()
+#write.table(CNsignalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")
diff -r 2b882515e1a3 -r b7f3854e08f8 markersSelection.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/markersSelection.py Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,34 @@
+import os
+import sys
+import subprocess
+
+def main():
+
+ inputdata=sys.argv[1]
+ response=sys.argv[2]
+ tmp_dir=sys.argv[3]
+ nbfold=sys.argv[4]
+ loss=sys.argv[5]
+ outputlog=sys.argv[6]
+ output=sys.argv[7]
+ log=sys.argv[8]
+
+ script_dir=os.path.dirname(os.path.abspath(__file__))
+
+ if (outputlog=="TRUE"):
+ errfile=open(log,'w')
+ else:
+ errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
+
+
+ retcode=subprocess.call(["Rscript", os.path.join(script_dir,"markersSelection.R"), inputdata, response, tmp_dir, nbfold, loss, output], stdout = errfile, stderr = errfile)
+
+# if (plot=="TRUE"):
+# shutil.copy(os.path.join(tmp_dir,"mpagenomics","Rplots.pdf"), pdffigures)
+
+ errfile.close()
+
+ sys.exit(retcode)
+
+if __name__ == "__main__":
+ main()
\ No newline at end of file
diff -r 2b882515e1a3 -r b7f3854e08f8 markersSelection.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/markersSelection.xml Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,100 @@
+
diff -r 2b882515e1a3 -r b7f3854e08f8 segcall.R
--- /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()
diff -r 2b882515e1a3 -r b7f3854e08f8 segcall.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/segcall.py Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,62 @@
+import os
+import sys
+import subprocess
+import zipfile
+
+
+def main():
+
+ input_file=sys.argv[2]
+ tmp_dir=sys.argv[4]
+ settingsType=sys.argv[6]
+ zip_file=sys.argv[9]
+ tumorcsv=sys.argv[10]
+ cellularity=sys.argv[11]
+ outputlog=sys.argv[12]
+ log=sys.argv[13]
+ user=sys.argv[14]
+ method=sys.argv[15]
+ script_dir=os.path.dirname(os.path.abspath(__file__))
+
+ iFile=open(input_file,'r')
+ dataSetLine=iFile.readline()
+ dataset=dataSetLine.split("\t")[1]
+ iFile.close()
+
+
+ if settingsType=="dataset":
+ settingsType=dataset
+
+ if (outputlog=="TRUE"):
+ errfile=open(log,'w')
+ else:
+ errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
+
+ fig_dir=os.path.join("mpagenomics",user,"figures",dataset,"segmentation/CN")
+
+ abs_fig_dir=os.path.join(tmp_dir,fig_dir)
+ if (os.path.isdir(abs_fig_dir)) and (sys.argv[7]=="TRUE"):
+ old_files=os.listdir(abs_fig_dir)
+ for ifile in old_files:
+ os.remove(os.path.join(abs_fig_dir,ifile))
+
+
+ retcode=subprocess.call(["Rscript", os.path.join(script_dir,"segcall.R"), sys.argv[1], dataset, sys.argv[3], sys.argv[4], sys.argv[5], settingsType, sys.argv[7], sys.argv[8], tumorcsv, cellularity, user, method], stdout = errfile, stderr = errfile)
+
+ errfile.close()
+
+ if (retcode == 0):
+ if (os.path.isdir(abs_fig_dir)) and (sys.argv[7]=="TRUE"):
+
+ new_files=os.listdir(abs_fig_dir)
+ zipbuf = zipfile.ZipFile(os.path.join(abs_fig_dir,zip_file), 'w', zipfile.ZIP_DEFLATED)
+ for current_file in new_files:
+ fn = os.path.join(abs_fig_dir,current_file)
+ relfn=fn[len(abs_fig_dir)+len(os.sep):]
+ zipbuf.write(fn,relfn)
+ sys.exit(retcode)
+ else:
+ sys.exit(retcode)
+
+if __name__ == "__main__":
+ main()
diff -r 2b882515e1a3 -r b7f3854e08f8 segcall.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/segcall.xml Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,198 @@
+
+ of the normalized data
+ mpagenomics
+
+ segcall.py '$chrom' '$input' '$output' '$__new_file_path__' '$nbcall'
+ #if $settings.settingsType == "file":
+ '$settings.inputs'
+ #end if
+ #if $settings.settingsType == "dataset":
+ '$settings.settingsType'
+ #end if
+ '$outputgraph' '$snp' '$zipfigures'
+ #if $settingsTumor.settingsTypeTumor == "standard":
+ 'none'
+ #end if
+ #if $settingsTumor.settingsTypeTumor == "tumor":
+ '$tumorcsv'
+ #end if
+ '$cellularity' '$outputlog' '$log' '$__user_id__' '$method'
+
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+ outputgraph == "TRUE"
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+ outputlog == "TRUE"
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+.. 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 2b882515e1a3 -r b7f3854e08f8 segmentation.R
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/segmentation.R Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,81 @@
+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)
+
+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$chrom)))
+ result=rbind(result,currentResult)
+ }
+ }
+}
+finalResult=data.frame(sampleNames=result["sampleNames"],chrom=result["chrom"],chromStart=result["chromStart"],chromEnd=result["chromEnd"],probes=result["probes"],means=result["means"],calls=result["calls"],stringsAsFactors=FALSE)
+sink(output)
+print(format(finalResult))
+sink()
+#write.table(finalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")
+} else {
+ result=data.frame(sampleNames=character(0),chrom=character(0),start=numeric(0),end=numeric(0),points=numeric(0),means=numeric(0),stringsAsFactors=FALSE)
+
+ for (chr in uniqueChr)
+ {
+ cat(paste0("chromosome ",chr,"\n"))
+ currentSubset=subset(CN, chromosome==chr)
+ currentPositions=currentSubset["position"]
+ for (sample in samples)
+ {
+ cat(paste0(" sample ",sample,"..."))
+ currentSignal=currentSubset[sample]
+ if (length(which(!is.na(unlist(currentSignal))))>1)
+ {
+ currentSeg=segmentation(signal=unlist(currentSignal),position=unlist(currentPositions),method=method)
+ currentResult=currentSeg$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)
+ sink(output)
+ print(format(finalResult))
+ sink()
+ #write.table(finalResult,output,row.names = FALSE, quote=FALSE, sep = "\t")
+}
+
diff -r 2b882515e1a3 -r b7f3854e08f8 segmentation.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/segmentation.py Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,78 @@
+import os
+import sys
+import subprocess
+import shutil
+import getopt
+
+
+def main(argv):
+
+ #default values
+ cellularity="1"
+ nbcall="3"
+
+ try:
+ opts, args = getopt.getopt(argv,"h:i:f:p:o:l:og:g:m:st:u:",["input=","new_file_path=","outputlog=","output=","log=","outputgraph=", "graph=", "method=", "signalType=", "user_id=", "nbcall=", "cellularity="])
+ except getopt.GetoptError as err:
+ print str(err)
+ sys.exit(2)
+ for opt, arg in opts:
+ if opt == '-h':
+ print 'segmentation.py'
+ sys.exit()
+ elif opt in ("-i", "--input"):
+ inputdata = arg
+ elif opt in ("-f", "--new_file_path"):
+ tmp_dir = arg
+ elif opt in ("-p", "--outputlog"):
+ outputlog = arg
+ elif opt in ("-o", "--output"):
+ output = arg
+ elif opt in ("-l", "--log"):
+ log = arg
+ elif opt in ("-og", "--outputgraph"):
+ plot = arg
+ elif opt in ("-g", "--graph"):
+ pdffigures = arg
+ elif opt in ("-m", "--method"):
+ method = arg
+ elif opt in ("-st", "--signalType"):
+ signalType = arg
+ elif opt in ("-u", "--user_id"):
+ userId = arg
+ elif opt in ("-c", "--nbcall"):
+ nbcall = arg
+ elif opt in ("-e", "--cellularity"):
+ cellularity = arg
+
+ #===========================================================================
+ # inputdata=sys.argv[1]
+ # tmp_dir=sys.argv[2]
+ # nbcall=sys.argv[3]
+ # cellularity=sys.argv[4]
+ # outputlog=sys.argv[5]
+ # output=sys.argv[6]
+ # log=sys.argv[7]
+ # plot=sys.argv[8]
+ # pdffigures=sys.argv[9]
+ # method=sys.argv[10]
+ #===========================================================================
+
+ script_dir=os.path.dirname(os.path.abspath(__file__))
+
+ if (outputlog=="TRUE"):
+ errfile=open(log,'w')
+ else:
+ errfile=open(os.path.join(tmp_dir,"errfile.log"),'w')
+
+ retcode=subprocess.call(["Rscript", os.path.join(script_dir,"segmentation.R"), inputdata, tmp_dir, nbcall, cellularity, output, method, userId, signalType], stdout = errfile, stderr = errfile)
+
+ if (plot=="TRUE"):
+ shutil.copy(os.path.join(tmp_dir,"mpagenomics",userId,"Rplots.pdf"), pdffigures)
+
+ errfile.close()
+
+ sys.exit(retcode)
+
+if __name__ == "__main__":
+ main(main(sys.argv[1:]))
\ No newline at end of file
diff -r 2b882515e1a3 -r b7f3854e08f8 segmentation.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/segmentation.xml Wed Apr 29 09:55:41 2015 +0200
@@ -0,0 +1,111 @@
+
+ of a previously normalized signal
+ mpagenomics
+
+ segmentation.py
+ #if $signalType.signal == "CN":
+ --nbcall '$signalType.nbcall'
+ --cellularity '$signalType.cellularity'
+ #else
+ --nbcall '3'
+ --cellularity '1.0'
+ #end if
+ --input '$input'
+ --new_file_path '$__new_file_path__'
+ --outputlog '$outputlog'
+ --output '$output'
+ --log '$log'
+ --outputgraph '$outputgraph'
+ --graph '$graph'
+ --method '$method'
+ --signalType '$signalType.signal'
+ --user_id '$__user_id__'
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 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>`_
+
+
+