Mercurial > repos > davidvanzessen > argalaxy_tools
comparison experimental_design/experimental_design.r @ 5:bcec7bb4e089 draft
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| author | davidvanzessen |
|---|---|
| date | Mon, 12 Dec 2016 05:22:57 -0500 |
| parents | afe85eb6572e |
| children | 106275b54470 |
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| 4:5ffd52fc35c4 | 5:bcec7bb4e089 |
|---|---|
| 1 args <- commandArgs(trailingOnly = TRUE) | |
| 2 | |
| 3 print(args) | |
| 4 | |
| 5 inputs = args[1:(length(args) - 1)] | |
| 6 output = args[length(args)] | |
| 7 | |
| 8 current.id = "" | |
| 9 counter = 1 | |
| 10 | |
| 11 result = NULL | |
| 12 | |
| 13 for(current in inputs){ | |
| 14 if(grepl("/", current)){ #its a path to a file | |
| 15 print(paste("Adding file", counter, "to", current.id)) | |
| 16 dat = read.table(current, sep="\t", header=T, quote="", fill=T) | |
| 17 | |
| 18 #IMGT check | |
| 19 | |
| 20 dat$Sample = current.id | |
| 21 dat$Replicate = counter | |
| 22 | |
| 23 if(is.null(result)){ | |
| 24 result = dat[NULL,] | |
| 25 } | |
| 26 | |
| 27 result = rbind(result, dat) | |
| 28 | |
| 29 counter = counter + 1 | |
| 30 | |
| 31 } else { #its an ID of a patient | |
| 32 print(paste("New patient", current)) | |
| 33 current.id = current | |
| 34 counter = 1 | |
| 35 } | |
| 36 } | |
| 37 | |
| 38 write.table(result, output, sep="\t", quote=F, row.names=F, col.names=T) |