view baseline/filter.r @ 4:477e95b098fd draft

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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)