Mercurial > repos > davidvanzessen > shm_csr
changeset 65:dc06e94bc1e3 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 06 Dec 2017 09:55:37 -0500 |
| parents | c6dd3215ebe0 |
| children | 43a1aa648537 |
| files | new_imgt.r |
| diffstat | 1 files changed, 6 insertions(+), 1 deletions(-) [+] |
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--- a/new_imgt.r Wed Dec 06 08:52:00 2017 -0500 +++ b/new_imgt.r Wed Dec 06 09:55:37 2017 -0500 @@ -4,7 +4,12 @@ merged.file = args[2] gene = args[3] -merged = read.table(merged.file, header=T, sep="\t", fill=T, stringsAsFactors=F, comment.char="") +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),]