# HG changeset patch
# User czouaoui
# Date 1526479860 14400
# Node ID 50809ff03c17b5cb30a57cf831c9420a64ac13c0
# Parent  3e855db19775c2619fa898929440a56dd03b0e08
Uploaded

diff -r 3e855db19775 -r 50809ff03c17 gc_cover_data/getGCCoverData.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gc_cover_data/getGCCoverData.R	Wed May 16 10:11:00 2018 -0400
@@ -0,0 +1,16 @@
+#!/usr/bin/env Rscript
+args = commandArgs(trailingOnly=TRUE)
+sessionInfo()
+library(Biostrings)
+sessionInfo()
+# test if there is at least one argument: if not, return an error
+if (length(args) != 3) {
+  stop("At least 3 arguments must be supplied (Fasta file, Coverage file, Fasta file name)", call.=FALSE)
+}
+
+seqString <- read.fasta(args[1], seqonly=TRUE)
+sequence <- DNAString(seqString[[1]])
+covData <- scan(args[2], integer(), sep =",", skip = 1)
+seqName <- strsplit(args[3], '[.].*')
+
+save(sequence, covData, seqName, file="gcCover.RData")