|
95
|
1 args <- commandArgs(trailingOnly = TRUE)
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2
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|
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3 imgt.dir = args[1]
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4 merged.file = args[2]
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|
99
|
5 gene = args[3]
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|
95
|
6
|
|
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7 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
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|
|
8
|
|
99
|
9 if(gene != "-"){
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10 merged = merged[grepl(gene, merged$best_match),]
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11 }
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|
|
12
|
|
97
|
13 merged = merged[!grepl("unmatched", merged$best_match),]
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|
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14
|
|
95
|
15 for(f in list.files(imgt.dir, pattern="*.txt$")){
|
|
105
|
16 #print(paste("filtering", f))
|
|
95
|
17 path = paste(imgt.dir, f, sep="")
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|
|
18 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F)
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|
|
19
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|
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20 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
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|
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21
|
|
105
|
22 if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file
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|
|
23 dat[,grepl("^FR1", names(dat))] = 0
|
|
95
|
24 }
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|
|
25
|
|
|
26 write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T)
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|
|
27 }
|
