Mercurial > repos > petr-novak > repeat_annotation_pipeline3
comparison split_and_filter_tracks.R @ 0:ea6a3059a6af draft
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author | petr-novak |
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date | Mon, 18 Oct 2021 11:01:20 +0000 |
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-1:000000000000 | 0:ea6a3059a6af |
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1 #!/usr/bin/env Rscript | |
2 suppressPackageStartupMessages(library(rtracklayer)) | |
3 gff = import(commandArgs(T)[1]) | |
4 BN = gsub("[.]gff(3){0,1}","",basename(commandArgs(T)[1])) | |
5 min_width = as.numeric(commandArgs(T)[2]) | |
6 outdir = commandArgs(T)[3] | |
7 | |
8 | |
9 | |
10 gff_min_width=gff[width(gff)>=min_width] | |
11 | |
12 | |
13 | |
14 dir.create(outdir, recursive = TRUE, showWarnings = FALSE) | |
15 | |
16 gff_min_width_parts = split(gff_min_width, f=gff_min_width$Name) | |
17 | |
18 x = sapply(names(gff_min_width_parts), | |
19 function(x) export( | |
20 gff_min_width_parts[[x]], | |
21 format="gff3", | |
22 con=paste0( | |
23 outdir,"/", | |
24 gsub("/","_",x), | |
25 "_", min_width ,"plus.gff3" | |
26 ) | |
27 )) | |
28 | |
29 |