Mercurial > repos > davidvanzessen > shm_csr
view naive_output.r @ 28:c0ecc31829bd draft
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author | davidvanzessen |
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date | Wed, 07 Dec 2016 08:17:09 -0500 |
parents | c33d93683a09 |
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args <- commandArgs(trailingOnly = TRUE) naive.file = args[1] shm.file = args[2] output.file.ca = args[3] output.file.cg = args[4] output.file.cm = args[5] naive = read.table(naive.file, sep="\t", header=T, quote="", fill=T) shm.merge = read.table(shm.file, sep="\t", header=T, quote="", fill=T) final = merge(naive, shm.merge[,c("Sequence.ID", "best_match")], by.x="ID", by.y="Sequence.ID") print(paste("nrow final:", nrow(final))) names(final)[names(final) == "best_match"] = "Sample" final.numeric = final[,sapply(final, is.numeric)] final.numeric[is.na(final.numeric)] = 0 final[,sapply(final, is.numeric)] = final.numeric final.ca = final[grepl("^ca", final$Sample),] final.cg = final[grepl("^cg", final$Sample),] final.cm = final[grepl("^cm", final$Sample),] if(nrow(final.ca) > 0){ final.ca$Replicate = 1 } if(nrow(final.cg) > 0){ final.cg$Replicate = 1 } if(nrow(final.cm) > 0){ final.cm$Replicate = 1 } #print(paste("nrow final:", nrow(final))) #final2 = final #final2$Sample = gsub("[0-9]", "", final2$Sample) #final = rbind(final, final2) #final$Replicate = 1 write.table(final.ca, output.file.ca, quote=F, sep="\t", row.names=F, col.names=T) write.table(final.cg, output.file.cg, quote=F, sep="\t", row.names=F, col.names=T) write.table(final.cm, output.file.cm, quote=F, sep="\t", row.names=F, col.names=T)