--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/get_tx2gene_table.R	Fri Oct 19 07:36:02 2018 -0400
@@ -0,0 +1,17 @@
+library(getopt)
+
+# we read the options from the default: commandArgs(TRUE).
+spec <- matrix(c(
+  "input_type", "t", 1, "character",
+  "outfile", "o", 1, "character",
+  "gtfFile", "x", 1, "character"),
+  byrow=TRUE, ncol=4)
+opt <- getopt(spec)
+
+suppressPackageStartupMessages({library("GenomicFeatures")})
+txdb <- makeTxDbFromGFF(opt$gtfFile, format=opt$input_type)
+k <- keys(txdb, keytype = "GENEID")
+df <- select(txdb, keys = k, keytype = "GENEID", columns = "TXNAME")
+tx2gene <- df[, 2:1] # tx ID, then gene ID
+write.table(tx2gene,file = opt$outfile, quote = FALSE, sep = " ",row.names = FALSE,col.names = FALSE)
+