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81
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1 arg = commandArgs(TRUE)
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2 summaryfile = arg[1]
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3 gappedfile = arg[2]
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4 selection = arg[3]
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5 output = arg[4]
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6 print(paste("selection = ", selection))
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7
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8
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9 summarydat = read.table(summaryfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote = "")
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10 gappeddat = read.table(gappedfile, header=T, sep="\t", fill=T, stringsAsFactors=F, quote = "")
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11
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12 fix_column_names = function(df){
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13 if("V.DOMAIN.Functionality" %in% names(df)){
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14 names(df)[names(df) == "V.DOMAIN.Functionality"] = "Functionality"
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15 print("found V.DOMAIN.Functionality, changed")
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16 }
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17 if("V.DOMAIN.Functionality.comment" %in% names(df)){
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18 names(df)[names(df) == "V.DOMAIN.Functionality.comment"] = "Functionality.comment"
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19 print("found V.DOMAIN.Functionality.comment, changed")
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20 }
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21 return(df)
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22 }
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23
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24 gappeddat = fix_column_names(gappeddat)
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25
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26 #dat = data.frame(merge(gappeddat, summarydat, by="Sequence.ID", all.x=T))
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27
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28 dat = cbind(gappeddat, summarydat$AA.JUNCTION)
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29
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30 colnames(dat)[length(dat)] = "AA.JUNCTION"
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31
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32 dat$VGene = gsub("^Homsap ", "", dat$V.GENE.and.allele)
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33 dat$VGene = gsub("[*].*", "", dat$VGene)
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34
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35 dat$DGene = gsub("^Homsap ", "", dat$D.GENE.and.allele)
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36 dat$DGene = gsub("[*].*", "", dat$DGene)
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37
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38 dat$JGene = gsub("^Homsap ", "", dat$J.GENE.and.allele)
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39 dat$JGene = gsub("[*].*", "", dat$JGene)
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40
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41 print(str(dat))
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42
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43 dat$past = do.call(paste, c(dat[unlist(strsplit(selection, ","))], sep = ":"))
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44
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45 dat = dat[!duplicated(dat$past), ]
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46
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47 print(paste("Sequences remaining after duplicate filter:", nrow(dat)))
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48
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49 dat = dat[dat$Functionality != "No results" & dat$Functionality != "unproductive",]
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50
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51 print(paste("Sequences remaining after functionality filter:", nrow(dat)))
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52
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53 print(paste("Sequences remaining:", nrow(dat)))
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54
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55 write.table(x=dat, file=output, sep="\t",quote=F,row.names=F,col.names=T)
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