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56
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1 args <- commandArgs(trailingOnly = TRUE) #first argument must be the summary file so it can grab the
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2
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3 current_file = args[1]
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4
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5 current = read.table(current_file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="", check.names=F)
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6
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7 if(!("Sequence number" %in% names(current))){
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8 stop("First argument doesn't contain the 'Sequence number' column")
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9 }
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10
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57
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11 tbl = table(current[,"Sequence ID"])
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56
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12 l_tbl = length(tbl)
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13 check = any(tbl > 1)
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14
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15 #if(l_tbl != nrow(current)){ # non unique IDs?
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16 if(check){
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17 print("Sequence.ID is not unique for every sequence, adding sequence number to IDs")
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18 for(i in 1:length(args)){
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19 current_file = args[i]
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20 print(paste("Appending 'Sequence number' column to 'Sequence ID' column in", current_file))
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21 current = read.table(current_file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="", check.names=F)
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22 current[,"Sequence ID"] = paste(current[,"Sequence ID"], current[,"Sequence number"], sep="_")
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23 write.table(x = current, file = current_file, quote = F, sep = "\t", na = "", row.names = F, col.names = T)
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24 }
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25 }
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