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3
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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, "------"))
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7
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8 summarydat = read.table(summaryfile, header=T, sep="\t", fill=T, stringsAsFactors=F)[,c("Sequence.ID", "AA.JUNCTION")]
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9 gappeddat = read.table(gappedfile, header=T, sep="\t", fill=T, stringsAsFactors=F)
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10 head(summarydat)
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11 head(gappeddat)
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12
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13 dat = merge(gappeddat, summarydat, by="Sequence.ID")
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14 head(dat)
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15
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16 dat$VGene = gsub("^Homsap ", "", dat$V.GENE.and.allele)
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17 dat$VGene = gsub("[*].*", "", dat$VGene)
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18
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19 dat$DGene = gsub("^Homsap ", "", dat$D.GENE.and.allele)
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20 dat$DGene = gsub("[*].*", "", dat$DGene)
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21
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22 dat$JGene = gsub("^Homsap ", "", dat$J.GENE.and.allele)
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23 dat$JGene = gsub("[*].*", "", dat$JGene)
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24
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25 dat$past = do.call(paste, c(dat[unlist(strsplit(selection, ","))], sep = ":"))
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26
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27 dat = dat[!duplicated(dat$past), ]
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28
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29 write.table(x=dat, file=output, sep="\t",quote=F,row.names=F,col.names=T)
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