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114
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1 args <- commandArgs(trailingOnly = TRUE)
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2
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3 imgt.dir = args[1]
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4 merged.file = args[2]
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5 gene = args[3]
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6
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7 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
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8
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9 if(gene != "-"){
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127
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10 merged = merged[grepl(paste("^", gene, sep=""), merged$best_match),]
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11 } else {
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12 merged = merged[!grepl("unmatched", merged$best_match),]
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114
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13 }
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14
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15 merged = merged[!grepl("unmatched", merged$best_match),]
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16
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17 for(f in list.files(imgt.dir, pattern="*.txt$")){
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18 #print(paste("filtering", f))
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19 path = paste(imgt.dir, f, sep="")
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20 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F, check.names=FALSE)
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21
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22 dat = dat[dat[,"Sequence ID"] %in% merged$Sequence.ID,]
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23
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24 if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file
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25 dat[,grepl("^FR1", names(dat))] = 0
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26 }
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27
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28 write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T, na="")
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29 }
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