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1 args <- commandArgs(trailingOnly = TRUE)
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2
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3 naive.file = args[1]
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4 shm.file = args[2]
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5 output.file.ca = args[3]
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6 output.file.cg = args[4]
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7 output.file.cm = args[5]
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8
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9 naive = read.table(naive.file, sep="\t", header=T, quote="", fill=T)
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10 shm.merge = read.table(shm.file, sep="\t", header=T, quote="", fill=T)
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11
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12
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13 final = merge(naive, shm.merge[,c("Sequence.ID", "best_match")], by.x="ID", by.y="Sequence.ID")
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14 print(paste("nrow final:", nrow(final)))
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15 names(final)[names(final) == "best_match"] = "Sample"
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16 final.numeric = final[,sapply(final, is.numeric)]
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17 final.numeric[is.na(final.numeric)] = 0
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18 final[,sapply(final, is.numeric)] = final.numeric
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19
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20 final.ca = final[grepl("^ca", final$Sample),]
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21 final.cg = final[grepl("^cg", final$Sample),]
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22 final.cm = final[grepl("^cm", final$Sample),]
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23
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24 if(nrow(final.ca) > 0){
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25 final.ca$Replicate = 1
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26 }
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27
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28 if(nrow(final.cg) > 0){
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29 final.cg$Replicate = 1
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30 }
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31
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32 if(nrow(final.cm) > 0){
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33 final.cm$Replicate = 1
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34 }
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35
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36 #print(paste("nrow final:", nrow(final)))
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37 #final2 = final
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38 #final2$Sample = gsub("[0-9]", "", final2$Sample)
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39 #final = rbind(final, final2)
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40 #final$Replicate = 1
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41
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42 write.table(final.ca, output.file.ca, quote=F, sep="\t", row.names=F, col.names=T)
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43 write.table(final.cg, output.file.cg, quote=F, sep="\t", row.names=F, col.names=T)
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44 write.table(final.cm, output.file.cm, quote=F, sep="\t", row.names=F, col.names=T)
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45
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