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2
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1 #!/usr/bin/env Rscript
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2
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3 suppressPackageStartupMessages(library("optparse"))
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4
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5 option_list <- list(
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6 make_option(c("-i", "--input"), action="store", dest="input", help="Input .bed.gz file produced by prepMat"),
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7 make_option(c("-o", "--output"), action="store", dest="output", help="Output file"),
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16
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8 make_option(c("-w", "--work_dir"), action="store", dest="work_dir", help="Working directory")
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2
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9 )
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10
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11 parser <- OptionParser(usage="%prog [options] file", option_list=option_list)
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12 args <- parse_args(parser, positional_arguments=TRUE)
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13 opt <- args$options
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14
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21
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15 #data_table <- read.table(opt$input)
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16 #as.matrix(data_table)
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17 #status <- match(data_table[,3], missing)
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18 #data_table[,3] <- paste(opt$work_dir, data_table[,1], ".", data_table[,2], ".bed.gz", sep="")
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19 #data_table <- data_table[is.na(status)==TRUE,]
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20 #write.table(array(data_table, dim=c(length(data_table)/3, 3)), file=opt$output, quote=FALSE, row.names=FALSE, col.names=FALSE)
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21
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22 x=as.matrix(read.table(opt$input))
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23 t=match(x[,3],missing)
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24 x[,3]=paste(opt$work_dir, x[,1],".",x[,2],".bed.gz", sep="")
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25 x=x[is.na(t)==T,]
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26 write.table(array(x,dim=c(length(x)/3,3)), opt$output, quote=F,row.names=F,col.names=F)
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