Mercurial > repos > davidvanzessen > extract_duplicates
comparison extract_duplicates.r @ 0:02cf2dd19564 draft
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| author | davidvanzessen |
|---|---|
| date | Fri, 21 Aug 2015 10:49:14 -0400 |
| parents | |
| children | a3c4e3e62e10 |
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| -1:000000000000 | 0:02cf2dd19564 |
|---|---|
| 1 args <- commandArgs(trailingOnly = TRUE) | |
| 2 | |
| 3 input=args[1] | |
| 4 column=as.numeric(args[2]) | |
| 5 header=(args[3] == "yes") | |
| 6 out_file=args[4] | |
| 7 | |
| 8 dat = read.table(input, header=header, sep="\t", fill=T, stringsAsFactors=F) | |
| 9 | |
| 10 duplicates = dat[duplicated(dat[,column]),column] | |
| 11 | |
| 12 dat = dat[dat[,column] %in% duplicates,] | |
| 13 | |
| 14 dat = dat[order(dat[,column]),] | |
| 15 | |
| 16 write.table(dat, out_file, sep="\t", row.names=F, col.names=header, quote=F) |