Mercurial > repos > davidvanzessen > argalaxy_tools
comparison new_imgt.r @ 4:5ffd52fc35c4 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 12 Dec 2016 05:22:37 -0500 |
| parents | |
| children |
comparison
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| 3:beaa487ecf43 | 4:5ffd52fc35c4 |
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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 } |