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1 #!/usr/bin/env Rscript
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2 suppressPackageStartupMessages(library(rtracklayer))
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3 gff = import(commandArgs(T)[1])
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4 BN = gsub("[.]gff(3){0,1}","",basename(commandArgs(T)[1]))
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5 min_width = as.numeric(commandArgs(T)[2])
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6 outdir = commandArgs(T)[3]
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7
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8
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9
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10 gff_min_width=gff[width(gff)>=min_width]
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11
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12
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13
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14 dir.create(outdir, recursive = TRUE, showWarnings = FALSE)
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15
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16 gff_min_width_parts = split(gff_min_width, f=gff_min_width$Name)
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17
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18 x = sapply(names(gff_min_width_parts),
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19 function(x) export(
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20 gff_min_width_parts[[x]],
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21 format="gff3",
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22 con=paste0(
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23 outdir,"/",
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24 gsub("/","_",x),
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25 "_", min_width ,"plus.gff3"
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26 )
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27 ))
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