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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$options
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14
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16
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15 r_matrix <- as.matrix(read.table(opt$input));
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16 status <- match(r_matrix[,3], missing);
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17 r_matrix[,3] <- paste(opt$work_dir, r_matrix[,1], ".", r_matrix[,2], ".bed.gz", sep="");
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17
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18 r_matrix <- r_matrix[is.na(status)==TRUE,];
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18
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19 write.table(array(r_matrix, dim=c(length(r_matrix)/3, 3)), file=opt$output, quote=FALSE, row.names=FALSE, col.names=FALSE);
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