--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_length_and_gc_content.r	Thu Nov 17 16:41:06 2016 -0500
@@ -0,0 +1,59 @@
+# originally by Devon Ryan, https://www.biostars.org/p/84467/
+
+options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
+
+# we need that to not crash galaxy with an UTF8 error on German LC settings.
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+
+suppressPackageStartupMessages({
+    library("GenomicRanges")
+    library("rtracklayer")
+    library("Rsamtools")
+    library("optparse")
+    library("data.table")
+})
+
+option_list <- list(
+    make_option(c("-g","--gtf"), type="character", help="Input GTF file with gene / exon information."),
+    make_option(c("-f","--fasta"), type="character", default=FALSE, help="Fasta file that corresponds to the supplied GTF."),
+    make_option(c("-l","--length"), type="character", default=FALSE, help="Output file with gene name and length."),
+    make_option(c("-gc","--gc_content"), type="character", default=FALSE, help="Output file with gene name and GC content.")
+  )
+
+parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
+args = parse_args(parser)
+
+GTFfile = args$gtf
+FASTAfile = args$fasta
+length = args$length
+gc_content = args$gc_content
+
+#Load the annotation and reduce it
+GTF <- import.gff(GTFfile, format="gtf", genome=NA, feature.type="exon")
+grl <- reduce(split(GTF, elementMetadata(GTF)$gene_id))
+reducedGTF <- unlist(grl, use.names=T)
+elementMetadata(reducedGTF)$gene_id <- rep(names(grl), elementNROWS(grl))
+
+#Open the fasta file
+FASTA <- FaFile(FASTAfile)
+open(FASTA)
+
+#Add the GC numbers
+elementMetadata(reducedGTF)$nGCs <- letterFrequency(getSeq(FASTA, reducedGTF), "GC")[,1]
+elementMetadata(reducedGTF)$widths <- width(reducedGTF)
+
+#Create a list of the ensembl_id/GC/length
+calc_GC_length <- function(x) {
+    nGCs = sum(elementMetadata(x)$nGCs)
+    width = sum(elementMetadata(x)$widths)
+    c(width, nGCs/width)
+}
+output <- t(sapply(split(reducedGTF, elementMetadata(reducedGTF)$gene_id), calc_GC_length))
+output <- data.frame(setDT(data.frame(output), keep.rownames = TRUE)[])
+
+
+write.table(output[,c(1,2)], file=length, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
+write.table(output[,c(1,3)], file=gc_content, col.names=FALSE, row.names=FALSE, quote=FALSE, sep="\t")
+
+
+sessionInfo()