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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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8 make_option(c("-w", "--work_dir"), action="store", dest="work_dir", help="Working directory"),
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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$options
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14
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15 input_dir = paste(opt$work_dir, "Input/", sep="");
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16 r_matrix = as.matrix(read.table(opt$input));
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17 status = match(r_matrix[,3], missing);
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18 r_matrix[,3] = paste(input_dir, r_matrix[,1], ".", r_matrix[,2], ".bed.gz", sep="");
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19 r_matrix = r_matrix[is.na(status)==T,];
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20 write.table(array(r_matrix, dim = c(length(r_matrix) / 3, 3)), opt$output, quote=F, row.names=F, col.names=F);
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