Mercurial > repos > petr-novak > repeat_annotation_pipeline3
diff clean_rm_output.R @ 1:814cba36e435 draft
Uploaded
| author | mvdbeek |
|---|---|
| date | Mon, 21 Feb 2022 10:21:39 +0000 |
| parents | ea6a3059a6af |
| children | 7f1032da7a0a |
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--- a/clean_rm_output.R Mon Oct 18 11:01:20 2021 +0000 +++ b/clean_rm_output.R Mon Feb 21 10:21:39 2022 +0000 @@ -1,5 +1,7 @@ #!/usr/bin/env Rscript suppressPackageStartupMessages(library(rtracklayer)) +suppressPackageStartupMessages(library(parallel)) + gff_cleanup = function(gff){ ## remove overlapin annotation track - assign new annot @@ -50,7 +52,7 @@ ## infile = "./test_data/raw_rm.out" -rm_out = read.table(infile, as.is=TRUE, sep="", skip = 2, fill=TRUE, header=FALSE) +rm_out = read.table(infile, as.is=TRUE, sep="", skip = 2, fill=TRUE, header=FALSE, col.names=paste0("V",1:16)) gff = GRanges(seqnames = rm_out$V5, ranges = IRanges(start = rm_out$V6, end=rm_out$V7))