--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/get_length_and_gc_content.r	Thu Feb 25 05:26:51 2016 -0500
@@ -0,0 +1,44 @@
+# originally by Devon Ryan, https://www.biostars.org/p/84467/
+
+library(GenomicRanges)
+library(rtracklayer)
+library(Rsamtools)
+library(optparse)
+
+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("-o","--output"), type="character", default=FALSE, help="Output file with gene name, length and GC content.")
+  )
+
+parser <- OptionParser(usage = "%prog [options] file", option_list=option_list)
+args = parse_args(parser)
+
+GTFfile = args.gtf
+FASTAfile = args.fasta
+output = args.output
+
+#Load the annotation and reduce it
+GTF <- import.gff(GTFfile, format="gtf", genome=NA, asRangedData=F, feature.type="exon")
+grl <- reduce(split(GTF, elementMetadata(GTF)$gene_name))
+reducedGTF <- unlist(grl, use.names=T)
+elementMetadata(reducedGTF)$gene_name <- rep(names(grl), elementLengths(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_name), calc_GC_length))
+colnames(output) <- c("Length", "GC")
+
+write.table(output, file="GC_lengths.tsv", sep="\t")
\ No newline at end of file