|
95
|
1 args <- commandArgs(trailingOnly = TRUE)
|
|
|
2
|
|
|
3 imgt.dir = args[1]
|
|
|
4 merged.file = args[2]
|
|
|
5
|
|
|
6 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
|
|
|
7
|
|
|
8 for(f in list.files(imgt.dir, pattern="*.txt$")){
|
|
|
9 print(paste("filtering", f))
|
|
|
10 path = paste(imgt.dir, f, sep="")
|
|
|
11 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F)
|
|
|
12
|
|
|
13 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
|
|
|
14
|
|
|
15 if("FR1.IMGT" %in% colnames(dat)){
|
|
|
16 dat$FR1.IMGT = ""
|
|
|
17 }
|
|
|
18
|
|
|
19 write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T)
|
|
|
20 }
|
