Mercurial > repos > davidvanzessen > argalaxy_tools

comparison naive_output.r @ 57:16c7fc1c4bf8 draft

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author davidvanzessen
date Fri, 18 Mar 2016 07:50:34 -0400
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56:2eb94c08e550 57:16c7fc1c4bf8
1 args <- commandArgs(trailingOnly = TRUE)
2
3 naive.file = args[1]
4 shm.file = args[2]
5 output.file = args[3]
6
7 naive = read.table(naive.file, sep="\t", header=T, quote="", fill=T)
8 shm.merge = read.table(shm.file, sep="\t", header=T, quote="", fill=T)
9
10
11 final = merge(naive, shm.merge[,c("Sequence.ID", "best_match")], by.x="ID", by.y="Sequence.ID")
12 print(paste("nrow final:", nrow(final)))
13 names(final)[names(final) == "best_match"] = "Sample"
14 final.numeric = final[,sapply(final, is.numeric)]
15 final.numeric[is.na(final.numeric)] = 0
16 final[,sapply(final, is.numeric)] = final.numeric
17 print(paste("nrow final:", nrow(final)))
18 final2 = final
19 final2$Sample = gsub("[0-9]", "", final2$Sample)
20 final = rbind(final, final2)
21 final$Replicate = 1
22
23 write.table(final, output.file, quote=F, sep="\t", row.names=F, col.names=T)