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52
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1 args <- commandArgs(trailingOnly = TRUE)
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2
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3 infile=args[1]
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4 outfile=args[2]
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5
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6 blasted = read.table(infile, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="")
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7
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8 blasted$ID = 1:nrow(blasted)
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9 blasted$VDJ.Frame = "Out-of-frame"
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10
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11 search = blasted$inFrame == "true" & blasted$noStop == "false"
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12 if(sum(search) > 0){
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13 blasted[search ,]$VDJ.Frame = "In-frame with stop codon"
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14 }
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15
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16 search = blasted$inFrame == "true" & blasted$noStop == "true"
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17 if(sum(search) > 0){
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18 blasted[search ,]$VDJ.Frame = "In-frame"
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19 }
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20
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21 blasted$Top.V.Gene = blasted$vSegment
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22 blasted$Top.D.Gene = blasted$dSegment
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23 blasted$Top.J.Gene = blasted$jSegment
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24 blasted$CDR1.Seq = blasted$cdr1aa
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25 blasted$CDR1.Length = nchar(blasted$CDR1.Seq)
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26 blasted$CDR2.Seq = blasted$cdr2aa
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27 blasted$CDR2.Length = nchar(blasted$CDR2.Seq)
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28 blasted$CDR3.Seq = blasted$cdr3aa
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29 blasted$CDR3.Length = nchar(blasted$CDR3.Seq)
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30 blasted$CDR3.Seq.DNA = blasted$cdr3nt
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31 blasted$CDR3.Length.DNA = nchar(blasted$CDR3.Seq.DNA)
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32 blasted$Strand = "+/-"
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33 blasted$CDR3.Found.How = "found"
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34
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35 search = blasted$cdr3nt == ""
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36 if(sum(search) > 0){
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37 blasted[search,]$CDR3.Found.How = "NOT_FOUND"
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38 }
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39
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40 blasted$AA.JUNCTION = blasted$CDR3.Seq
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41
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42 n = c("X.reads_count", "ID", "VDJ.Frame", "Top.V.Gene", "Top.D.Gene", "Top.J.Gene", "CDR1.Seq", "CDR1.Length", "CDR2.Seq", "CDR2.Length", "CDR3.Seq", "CDR3.Length", "CDR3.Seq.DNA", "CDR3.Length.DNA", "Strand", "CDR3.Found.How", "Functionality", "AA.JUNCTION")
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43
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44 n[!(n %in% names(blasted))]
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45
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46 blasted = blasted[,c("X.reads_count", "ID", "VDJ.Frame", "Top.V.Gene", "Top.D.Gene", "Top.J.Gene", "CDR1.Seq", "CDR1.Length", "CDR2.Seq", "CDR2.Length", "CDR3.Seq", "CDR3.Length", "CDR3.Seq.DNA", "CDR3.Length.DNA", "Strand", "CDR3.Found.How", "AA.JUNCTION")]
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47
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48 names(blasted) = c("frequency.count", "ID", "VDJ Frame", "Top V Gene", "Top D Gene", "Top J Gene", "CDR1 Seq", "CDR1 Length", "CDR2 Seq", "CDR2 Length", "CDR3 Seq", "CDR3 Length", "CDR3 Seq DNA", "CDR3 Length DNA", "Strand", "CDR3 Found How", "AA JUNCTION")
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49
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50 #duplicate rows based on frequency.count
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51 blasted = blasted[rep(seq_len(nrow(blasted)), blasted$frequency.count),]
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52 blasted$ID = 1:nrow(blasted)
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53
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54 blasted = blasted[,c("ID", "VDJ Frame", "Top V Gene", "Top D Gene", "Top J Gene", "CDR1 Seq", "CDR1 Length", "CDR2 Seq", "CDR2 Length", "CDR3 Seq", "CDR3 Length", "CDR3 Seq DNA", "CDR3 Length DNA", "Strand", "CDR3 Found How", "AA JUNCTION")]
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55
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56 write.table(blasted, outfile, quote=F, sep="\t", row.names=F, col.names=T)
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