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annotate gff2tabular.R @ 3:1069776f7ae2 draft default tip

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planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 3b9f93ed06cc32dbfa271789739e7a1e8fac528c
author petr-novak
date Tue, 30 Apr 2024 08:27:27 +0000
parents 639c0edb7e64
children
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696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
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1 #!/usr/bin/env Rscript
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
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2 library(rtracklayer)
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
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3 gff <- import(commandArgs(T)[1], format='GFF')
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
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4 tabular <- as.data.frame(gff)
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639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
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5 head(tabular)
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
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6 # some columns are lists, we need to convert them to vectors before writing to file
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
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7 for (i in 1:ncol(tabular)){
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
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8 if (is.list(tabular[[i]])){
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
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9 tabular[[i]] <- sapply(tabular[[i]], function(x) paste(x, collapse = ";"))
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
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10 }
639c0edb7e64 planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
petr-novak
parents: 0
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11 }
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696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
petr-novak
parents:
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12 write.table(tabular, file = commandArgs(T)[2], quote=FALSE, sep="\t", row.names=FALSE)
696e702ebf74 "planemo upload commit 0f6eca49bafc3c946189d793161a7f81d595e1a1-dirty"
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13