Mercurial > repos > petr-novak > various_galaxy_tools
view gff2tabular.R @ 1:639c0edb7e64 draft
planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 248ffeb6792d5807820b664eae3e88306f3f395e-dirty
author | petr-novak |
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date | Mon, 26 Feb 2024 12:59:20 +0000 |
parents | 696e702ebf74 |
children |
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#!/usr/bin/env Rscript library(rtracklayer) gff <- import(commandArgs(T)[1], format='GFF') tabular <- as.data.frame(gff) head(tabular) # some columns are lists, we need to convert them to vectors before writing to file for (i in 1:ncol(tabular)){ if (is.list(tabular[[i]])){ tabular[[i]] <- sapply(tabular[[i]], function(x) paste(x, collapse = ";")) } } write.table(tabular, file = commandArgs(T)[2], quote=FALSE, sep="\t", row.names=FALSE)