Mercurial > repos > davidvanzessen > mutation_analysis
comparison baseline/filter.r @ 0:8a5a2abbb870 draft default tip
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| author | davidvanzessen |
|---|---|
| date | Mon, 29 Aug 2016 05:36:10 -0400 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:8a5a2abbb870 |
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| 1 arg = commandArgs(TRUE) | |
| 2 summaryfile = arg[1] | |
| 3 gappedfile = arg[2] | |
| 4 selection = arg[3] | |
| 5 output = arg[4] | |
| 6 print(paste("selection = ", selection)) | |
| 7 | |
| 8 | |
| 9 summarydat = read.table(summaryfile, header=T, sep="\t", fill=T, stringsAsFactors=F) | |
| 10 gappeddat = read.table(gappedfile, header=T, sep="\t", fill=T, stringsAsFactors=F) | |
| 11 | |
| 12 #dat = data.frame(merge(gappeddat, summarydat, by="Sequence.ID", all.x=T)) | |
| 13 | |
| 14 dat = cbind(gappeddat, summarydat$AA.JUNCTION) | |
| 15 | |
| 16 colnames(dat)[length(dat)] = "AA.JUNCTION" | |
| 17 | |
| 18 dat$VGene = gsub("^Homsap ", "", dat$V.GENE.and.allele) | |
| 19 dat$VGene = gsub("[*].*", "", dat$VGene) | |
| 20 | |
| 21 dat$DGene = gsub("^Homsap ", "", dat$D.GENE.and.allele) | |
| 22 dat$DGene = gsub("[*].*", "", dat$DGene) | |
| 23 | |
| 24 dat$JGene = gsub("^Homsap ", "", dat$J.GENE.and.allele) | |
| 25 dat$JGene = gsub("[*].*", "", dat$JGene) | |
| 26 | |
| 27 #print(str(dat)) | |
| 28 | |
| 29 dat$past = do.call(paste, c(dat[unlist(strsplit(selection, ","))], sep = ":")) | |
| 30 | |
| 31 dat = dat[!duplicated(dat$past), ] | |
| 32 | |
| 33 dat = dat[dat$Functionality != "No results" & dat$Functionality != "unproductive",] | |
| 34 | |
| 35 write.table(x=dat, file=output, sep="\t",quote=F,row.names=F,col.names=T) |