Mercurial > repos > petrn > repeat_annotation_pipeline

annotate get_gff_part.R @ 0:d14182506989 draft default tip

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"planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
author petrn
date Tue, 15 Feb 2022 16:44:31 +0000
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d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
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1 #!/usr/bin/env Rscript
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
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2 suppressPackageStartupMessages(library(rtracklayer))
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
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3 g = import(commandArgs(T)[1])
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
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4 gd = mcols(g)
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
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5 col_name=commandArgs(T)[2]
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
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6 col_value=commandArgs(T)[3]
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
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7 inc = gd[,col_name] %in% col_value
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
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8 g_part = sort(sortSeqlevels(g[inc]))
d14182506989 "planemo upload commit d7966a292ed4209f4058e77ab8c0e49a67847b16-dirty"
petrn
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9 export(g_part, format = 'gff3', commandArgs(T)[4])