Mercurial > repos > davidvanzessen > mutation_analysis

comparison tmp/igat.r @ 99:86206431cbb0 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Thu, 16 Jun 2016 10:01:54 -0400
parents 6e8dfbe164c6
children 3cffb8a38bb1
comparison
equal deleted inserted replaced
98:5ffbf40cdd4b 99:86206431cbb0
1 args <- commandArgs(trailingOnly = TRUE) 1 args <- commandArgs(trailingOnly = TRUE)
2 2
3 imgt.dir = args[1] 3 imgt.dir = args[1]
4 merged.file = args[2] 4 merged.file = args[2]
5 gene = args[3]
5 6
6 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F) 7 merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F)
8
9 if(gene != "-"){
10 merged = merged[grepl(gene, merged$best_match),]
11 }
7 12
8 merged = merged[!grepl("unmatched", merged$best_match),] 13 merged = merged[!grepl("unmatched", merged$best_match),]
9 14
10 for(f in list.files(imgt.dir, pattern="*.txt$")){ 15 for(f in list.files(imgt.dir, pattern="*.txt$")){
11 print(paste("filtering", f)) 16 print(paste("filtering", f))
12 path = paste(imgt.dir, f, sep="") 17 path = paste(imgt.dir, f, sep="")
13 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F) 18 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F)
14 19
15 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,] 20 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
16 21
17 if("FR1.IMGT" %in% colnames(dat)){ 22 if(nrow(dat) > 0 & "FR1.IMGT" %in% colnames(dat)){
18 dat$FR1.IMGT = "" 23 dat$FR1.IMGT = ""
19 } 24 }
20 25
21 write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T) 26 write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T)
22 } 27 }