--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/getgo.r	Sun Feb 28 11:52:10 2016 -0500
@@ -0,0 +1,35 @@
+suppressWarnings(suppressMessages(library(goseq)))
+suppressWarnings(suppressMessages(library(optparse)))
+suppressWarnings(suppressMessages(library(rtracklayer)))
+suppressWarnings(suppressMessages(library(reshape2)))
+sink(stdout(), type = "message")
+
+option_list <- list(
+    make_option(c("-gtf", "--gtf"), type="character", help = "Path to GTF file for which to fetch GO data"),
+    make_option(c("-g", "--genome"), type="character", help = "Genome [used for looking up GO categories]"),
+    make_option(c("-i", "--gene_id"), type="character", help="Gene ID format"),
+    make_option(c("-c", "--cats"), type="character", help="Comma-seperated list of categories to fetch"),
+    make_option(c("-o", "--output"), type="character", help="Path to output file")
+)
+
+parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
+args = parse_args(parser)
+
+# Vars:
+
+gtf = args$gtf
+genome = args$genome
+gene_id = args$gene_id
+output = args$output
+cats = unlist(strsplit(args$cats, ','))
+genes = unique(import.gff(gtf)$gene_id)
+go_categories = getgo(genes, genome, id, fetch.cats=cats)
+
+# transform go category list to sth. more manipulatable in galaxy
+go_categories <- lapply(go_categories, unlist)
+go_categories = goseq:::reversemapping(go_categories)
+go_categories = melt(go_categories)
+colnames(go_categories) = c("#gene_id", "go_category")
+
+write.table(go_categories, output, sep="\t", row.names = FALSE, quote = FALSE)
+sessionInfo()
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