Mercurial > repos > petr-novak > repeat_annotation_pipeline3

annotate get_gff_part.R @ 0:ea6a3059a6af draft

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author petr-novak
date Mon, 18 Oct 2021 11:01:20 +0000
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1 #!/usr/bin/env Rscript
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2 suppressPackageStartupMessages(library(rtracklayer))
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3 g = import(commandArgs(T)[1])
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4 gd = mcols(g)
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5 col_name=commandArgs(T)[2]
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6 col_value=commandArgs(T)[3]
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7 inc = gd[,col_name] %in% col_value
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8 g_part = sort(sortSeqlevels(g[inc]))
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9 export(g_part, format = 'gff3', commandArgs(T)[4])