Mercurial > repos > davidvanzessen > mutation_analysis

comparison tmp/igat.r @ 105:e4957ad476a2 draft

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Uploaded
author davidvanzessen
date Thu, 23 Jun 2016 03:58:03 -0400
parents e6bc976760d4
children ade5cf6fd2dc
comparison
equal deleted inserted replaced
104:603a10976e9c 105:e4957ad476a2
11 } 11 }
12 12
13 merged = merged[!grepl("unmatched", merged$best_match),] 13 merged = merged[!grepl("unmatched", merged$best_match),]
14 14
15 for(f in list.files(imgt.dir, pattern="*.txt$")){ 15 for(f in list.files(imgt.dir, pattern="*.txt$")){
16 print(paste("filtering", f)) 16 #print(paste("filtering", f))
17 path = paste(imgt.dir, f, sep="") 17 path = paste(imgt.dir, f, sep="")
18 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)
19 19
20 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,] 20 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
21 21
22 if(nrow(dat) > 0 & "FR1.IMGT" %in% colnames(dat)){ 22 if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file
23 dat$FR1.IMGT = "" 23 dat[,grepl("^FR1", names(dat))] = 0
24 } 24 }
25 25
26 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)
27 } 27 }