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1 args<-commandArgs(TRUE)
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2
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3 chrom=args[1]
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4 dataset=args[2]
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5 output=args[3]
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6 tmp_dir=args[4]
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7 nbcall=as.numeric(args[5])
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8 input=args[6]
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9 outputfigures=type.convert(args[7])
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10 snp=type.convert(args[8])
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11 tumorcsv=args[9]
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12 cellularity=as.numeric(args[10])
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13 user=args[11]
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14 method=args[12]
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15
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16 library(MPAgenomics)
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17 workdir=file.path(tmp_dir, "mpagenomics",user)
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18 setwd(workdir)
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19
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20 if (grepl("all",tolower(chrom)) | chrom=="None") {
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21 chrom_vec=c(1:25)
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22 } else {
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23 chrom_tmp <- strsplit(chrom,",")
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24 chrom_vecstring <-unlist(chrom_tmp)
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25 chrom_vec <- as.numeric(chrom_vecstring)
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26 }
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27
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28 input_tmp <- strsplit(input,",")
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29 input_tmp_vecstring <-unlist(input_tmp)
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30
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31
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32 input_vecstring = sub("^([^.]*).*", "\\1", input_tmp_vecstring)
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33
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34 if (dataset == input) {
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35 if (tumorcsv== "none")
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36 {
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37 segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, nclass=nbcall, savePlot=outputfigures,onlySNP=snp, cellularity=cellularity, method=method)
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38 } else {
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39 segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, nclass=nbcall, savePlot=outputfigures,onlySNP=snp, cellularity=cellularity, method=method)
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40 }
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41 } else {
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42 if (tumorcsv== "none")
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43 {
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44 segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, listOfFiles=input_vecstring, nclass=nbcall, savePlot=outputfigures, onlySNP=snp, cellularity=cellularity, method=method)
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45 } else {
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46 segcall=cnSegCallingProcess(dataset,chromosome=chrom_vec, normalTumorArray=tumorcsv, listOfFiles=input_vecstring, nclass=nbcall, savePlot=outputfigures, onlySNP=snp, cellularity=cellularity, method=method)
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47 }
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48 }
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49
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50 sink(output)
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51 print(format(segcall))
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52 sink()
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53 #write.table(format(segcall),output,row.names = FALSE, quote=FALSE, sep = "\t")
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54 #write.fwf(segcall,output,rownames = FALSE, quote=FALSE, sep = "\t")
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55 quit()
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