Mercurial > repos > petr-novak > repeat_annotation_pipeline3
view 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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#!/usr/bin/env Rscript suppressPackageStartupMessages(library(rtracklayer)) gff = import(commandArgs(T)[1]) BN = gsub("[.]gff(3){0,1}","",basename(commandArgs(T)[1])) min_width = as.numeric(commandArgs(T)[2]) outdir = commandArgs(T)[3] gff_min_width=gff[width(gff)>=min_width] dir.create(outdir, recursive = TRUE, showWarnings = FALSE) gff_min_width_parts = split(gff_min_width, f=gff_min_width$Name) x = sapply(names(gff_min_width_parts), function(x) export( gff_min_width_parts[[x]], format="gff3", con=paste0( outdir,"/", gsub("/","_",x), "_", min_width ,"plus.gff3" ) ))