Mercurial > repos > petr-novak > repeat_annotation_pipeline3
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/split_and_filter_tracks.R Mon Oct 18 11:01:20 2021 +0000 @@ -0,0 +1,29 @@ +#!/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" + ) + )) + +