Mercurial > repos > davidvanzessen > shm_csr
view baseline/filter.r @ 50:75ee66a691a0 draft
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author | davidvanzessen |
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date | Mon, 15 May 2017 03:13:16 -0400 |
parents | c33d93683a09 |
children | 8728284105ee |
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arg = commandArgs(TRUE) summaryfile = arg[1] gappedfile = arg[2] selection = arg[3] output = arg[4] print(paste("selection = ", selection)) summarydat = read.table(summaryfile, header=T, sep="\t", fill=T, stringsAsFactors=F) gappeddat = read.table(gappedfile, header=T, sep="\t", fill=T, stringsAsFactors=F) #dat = data.frame(merge(gappeddat, summarydat, by="Sequence.ID", all.x=T)) dat = cbind(gappeddat, summarydat$AA.JUNCTION) colnames(dat)[length(dat)] = "AA.JUNCTION" dat$VGene = gsub("^Homsap ", "", dat$V.GENE.and.allele) dat$VGene = gsub("[*].*", "", dat$VGene) dat$DGene = gsub("^Homsap ", "", dat$D.GENE.and.allele) dat$DGene = gsub("[*].*", "", dat$DGene) dat$JGene = gsub("^Homsap ", "", dat$J.GENE.and.allele) dat$JGene = gsub("[*].*", "", dat$JGene) #print(str(dat)) dat$past = do.call(paste, c(dat[unlist(strsplit(selection, ","))], sep = ":")) dat = dat[!duplicated(dat$past), ] dat = dat[dat$Functionality != "No results" & dat$Functionality != "unproductive",] write.table(x=dat, file=output, sep="\t",quote=F,row.names=F,col.names=T)