Mercurial > repos > davidvanzessen > shm_csr
comparison new_imgt.r @ 81:b6f9a640e098 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Fri, 19 Feb 2021 15:10:54 +0000 |
| parents | |
| children |
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| 80:a4617f1d1d89 | 81:b6f9a640e098 |
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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, comment.char="", quote="") | |
| 8 | |
| 9 if(!("Sequence.ID" %in% names(merged))){ #change-o db | |
| 10 print("Change-O DB changing 'SEQUENCE_ID' to 'Sequence.ID'") | |
| 11 names(merged)[which(names[merged] == "SEQUENCE_ID")] = "Sequence.ID" | |
| 12 } | |
| 13 | |
| 14 if(gene != "-"){ | |
| 15 merged = merged[grepl(paste("^", gene, sep=""), merged$best_match),] | |
| 16 } | |
| 17 | |
| 18 if("best_match" %in% names(merged)){ | |
| 19 merged = merged[!grepl("unmatched", merged$best_match),] | |
| 20 } | |
| 21 | |
| 22 nrow_dat = 0 | |
| 23 | |
| 24 for(f in list.files(imgt.dir, pattern="*.txt$")){ | |
| 25 #print(paste("filtering", f)) | |
| 26 path = file.path(imgt.dir, f) | |
| 27 dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F, check.names=FALSE, comment.char="") | |
| 28 | |
| 29 dat = dat[dat[,"Sequence ID"] %in% merged$Sequence.ID,] | |
| 30 | |
| 31 nrow_dat = nrow(dat) | |
| 32 | |
| 33 if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file | |
| 34 dat[,grepl("^FR1", names(dat))] = 0 | |
| 35 } | |
| 36 | |
| 37 write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T, na="") | |
| 38 } | |
| 39 | |
| 40 print(paste("Creating new zip for ", gene, "with", nrow_dat, "sequences")) |