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47
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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 = args[3]
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6
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7 naive = read.table(naive.file, sep="\t", header=T, quote="", fill=T)
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8 shm.merge = read.table(shm.file, sep="\t", header=T, quote="", fill=T)
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9
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10
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11 final = merge(naive, shm.merge[,c("Sequence.ID", "best_match")], by.x="ID", by.y="Sequence.ID")
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12 print(paste("nrow final:", nrow(final)))
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13 names(final)[names(final) == "best_match"] = "Sample"
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14 final.numeric = final[,sapply(final, is.numeric)]
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15 final.numeric[is.na(final.numeric)] = 0
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16 final[,sapply(final, is.numeric)] = final.numeric
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17 print(paste("nrow final:", nrow(final)))
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18 final2 = final
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19 final2$Sample = gsub("[0-9]", "", final2$Sample)
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20 final = rbind(final, final2)
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21 final$Replicate = 1
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22
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23 write.table(final, output.file, quote=F, sep="\t", row.names=F, col.names=T)
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