Mercurial > repos > davidvanzessen > mutation_analysis
comparison tmp/igat.r @ 95:a66eb1c5374c draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 08 Jun 2016 03:54:49 -0400 |
| parents | |
| children | 6e8dfbe164c6 |
comparison
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| 94:e39176ccddc8 | 95:a66eb1c5374c |
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| 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 } |