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0
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1 args <- commandArgs(trailingOnly = TRUE)
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2
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3 print(args)
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4
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5 inputs = args[1:(length(args) - 1)]
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6 output = args[length(args)]
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7
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8 current.id = ""
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9 counter = 1
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10
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11 result = NULL
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12
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13 for(current in inputs){
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14 if(grepl("/", current)){ #its a path to a file
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15 print(paste("Adding file", counter, "to", current.id))
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16 dat = read.table(current, sep="\t", header=T, quote="", fill=T)
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17
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40
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18 if(nrow(dat) == 0){
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19 print(paste(counter, "of", current.id, "has no sequences, skipping"))
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20 next
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21 }
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22
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0
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23 #IMGT check
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24
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25 dat$Sample = current.id
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26 dat$Replicate = counter
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27
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28 if(is.null(result)){
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29 result = dat[NULL,]
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30 }
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31
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32 result = rbind(result, dat)
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33
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34 counter = counter + 1
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35
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36 } else { #its an ID of a patient
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37 print(paste("New patient", current))
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38 current.id = current
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39 counter = 1
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40 }
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41 }
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42
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43 write.table(result, output, sep="\t", quote=F, row.names=F, col.names=T)
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