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1
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1 args <- commandArgs(trailingOnly = TRUE)
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2
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3 files <- read.table(args[1], stringsAsFactors=F)
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4
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5 my.read.table <- function(file) {
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6 read.table(
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7 file,
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8 sep="\t",
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9 stringsAsFactors=T,
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10 header=as.logical(args[4])
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11 )
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12 }
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13
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14 data <- NA;
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15 if (length(files) == 1) {
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16 data <- my.read.table(files[1])
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17 }
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18 else {
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19 data_list <- apply(files, 1, my.read.table)
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20 data <- Reduce(function(x,y) { rbind(x,y) }, data_list)
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21 }
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22
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23 contig_order <- read.table(args[2], stringsAsFactors=F)[,1]
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24 data[,1] <- factor(data[,1], levels=contig_order)
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25 data <- data[order(data[,1]),]
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26 data[,1] <- as.character(data[,1])
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27
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28 write.table(
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29 x=data,
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30 file=args[3],
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31 sep ="\t",
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32 quote=F,
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33 row.names=F,
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34 col.names=as.logical(args[4])
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35 )
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