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