Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison clean_rm_output.R @ 1:814cba36e435 draft
Uploaded
| author | mvdbeek |
|---|---|
| date | Mon, 21 Feb 2022 10:21:39 +0000 |
| parents | ea6a3059a6af |
| children | 7f1032da7a0a |
comparison
equal
deleted
inserted
replaced
| 0:ea6a3059a6af | 1:814cba36e435 |
|---|---|
| 1 #!/usr/bin/env Rscript | 1 #!/usr/bin/env Rscript |
| 2 suppressPackageStartupMessages(library(rtracklayer)) | 2 suppressPackageStartupMessages(library(rtracklayer)) |
| 3 suppressPackageStartupMessages(library(parallel)) | |
| 4 | |
| 3 | 5 |
| 4 gff_cleanup = function(gff){ | 6 gff_cleanup = function(gff){ |
| 5 ## remove overlapin annotation track - assign new annot | 7 ## remove overlapin annotation track - assign new annot |
| 6 gff_disjoin = disjoin(gff, with.revmap=TRUE) | 8 gff_disjoin = disjoin(gff, with.revmap=TRUE) |
| 7 ## append annotation: | 9 ## append annotation: |
| 48 infile = commandArgs(T)[1] | 50 infile = commandArgs(T)[1] |
| 49 outfile = commandArgs(T)[2] | 51 outfile = commandArgs(T)[2] |
| 50 | 52 |
| 51 ## infile = "./test_data/raw_rm.out" | 53 ## infile = "./test_data/raw_rm.out" |
| 52 | 54 |
| 53 rm_out = read.table(infile, as.is=TRUE, sep="", skip = 2, fill=TRUE, header=FALSE) | 55 rm_out = read.table(infile, as.is=TRUE, sep="", skip = 2, fill=TRUE, header=FALSE, col.names=paste0("V",1:16)) |
| 54 | 56 |
| 55 gff = GRanges(seqnames = rm_out$V5, ranges = IRanges(start = rm_out$V6, end=rm_out$V7)) | 57 gff = GRanges(seqnames = rm_out$V5, ranges = IRanges(start = rm_out$V6, end=rm_out$V7)) |
| 56 | 58 |
| 57 # repeat class after # symbol - syntax 1 | 59 # repeat class after # symbol - syntax 1 |
| 58 gff$Name=rm_out$V11 | 60 gff$Name=rm_out$V11 |