Mercurial > repos > davidvanzessen > shm_csr
comparison new_imgt.r @ 0:c33d93683a09 draft
Uploaded
author | davidvanzessen |
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date | Thu, 13 Oct 2016 10:52:24 -0400 |
parents | |
children | fe44a905aee9 |
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-1:000000000000 | 0:c33d93683a09 |
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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 } |