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95
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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
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6 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
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7
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97
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8 merged = merged[!grepl("unmatched", merged$best_match),]
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9
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95
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10 for(f in list.files(imgt.dir, pattern="*.txt$")){
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11 print(paste("filtering", f))
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12 path = paste(imgt.dir, f, sep="")
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13 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F)
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14
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15 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
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16
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17 if("FR1.IMGT" %in% colnames(dat)){
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18 dat$FR1.IMGT = ""
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19 }
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20
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21 write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T)
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22 }
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