Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison clean_rm_output.R @ 1:814cba36e435 draft
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author | mvdbeek |
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date | Mon, 21 Feb 2022 10:21:39 +0000 |
parents | ea6a3059a6af |
children | 7f1032da7a0a |
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0:ea6a3059a6af | 1:814cba36e435 |
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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 |