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30
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1 sink(file="/tmp/none")
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2 sink("/dev/null")
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3 options(warn=-1)
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4 options(echo=F)
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5
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6 #invisible("EBSeq")
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7 #suppressMessages(library("EBSeq")) ##cms - changed on 11/11/13. Don't need EBSeq package.
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8
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9 args <- commandArgs(trailingOnly = T)
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10 inputfile <- args[1]
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11 Idx <- args[2]
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12 outputfile <- args[3]
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13
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14 print(args)
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15
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16 ReadIn=read.table(inputfile,stringsAsFactors=F,header=T, sep="\t")
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17
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18 IndexIn=strsplit(Idx,split=",")[[1]]
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19 Index=as.numeric(IndexIn)
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20
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21 #Mat=data.matrix(ReadIn)
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22 Mat=data.matrix(ReadIn[,-1]) ##cms - changed on 11/11/13. Otherwise pattern IDs are replaced with NA.
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23 rownames(Mat)=ReadIn[,1] ##cms - also added on 11/11/13 to add pattern IDs back in.
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24
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25 Out=Mat[Index,]
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26
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27
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28 #write.table(Out,file=outputfile,quote=F,col.names=T,row.names=T,sep = "\t")
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29 write.table(Out,file=outputfile,quote=F,col.names=NA,row.names=T,sep = "\t") ##cms - changed on 11/11/13
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30
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