Mercurial > repos > davidvanzessen > shm_csr
view new_imgt.r @ 72:c787e79e8b90 draft
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author | davidvanzessen |
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date | Tue, 05 Feb 2019 03:26:41 -0500 |
parents | dc06e94bc1e3 |
children |
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args <- commandArgs(trailingOnly = TRUE) imgt.dir = args[1] merged.file = args[2] gene = args[3] merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="", quote="") if(!("Sequence.ID" %in% names(merged))){ #change-o db print("Change-O DB changing 'SEQUENCE_ID' to 'Sequence.ID'") names(merged)[which(names[merged] == "SEQUENCE_ID")] = "Sequence.ID" } if(gene != "-"){ merged = merged[grepl(paste("^", gene, sep=""), merged$best_match),] } if("best_match" %in% names(merged)){ merged = merged[!grepl("unmatched", merged$best_match),] } nrow_dat = 0 for(f in list.files(imgt.dir, pattern="*.txt$")){ #print(paste("filtering", f)) path = file.path(imgt.dir, f) dat = read.table(path, header=T, sep="\t", fill=T, quote="", stringsAsFactors=F, check.names=FALSE, comment.char="") dat = dat[dat[,"Sequence ID"] %in% merged$Sequence.ID,] nrow_dat = nrow(dat) if(nrow(dat) > 0 & grepl("^8_", f)){ #change the FR1 columns to 0 in the "8_..." file dat[,grepl("^FR1", names(dat))] = 0 } write.table(dat, path, quote=F, sep="\t", row.names=F, col.names=T, na="") } print(paste("Creating new zip for ", gene, "with", nrow_dat, "sequences"))