From 0b10ee4c512f4477c0306dc0446969b25c8a0b84 Mon Sep 17 00:00:00 2001
From: borauyar <bora.uyar@mdc-berlin.de>
Date: Sat, 4 Sep 2021 11:47:07 +0200
Subject: [PATCH] restore export_bigwig.R script. could be used instead of
 deepTools bamCoverage

---
 scripts/export_bigwig.R | 64 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 64 insertions(+)
 create mode 100644 scripts/export_bigwig.R

diff --git a/scripts/export_bigwig.R b/scripts/export_bigwig.R
new file mode 100644
index 0000000..6129ca9
--- /dev/null
+++ b/scripts/export_bigwig.R
@@ -0,0 +1,64 @@
+Gx RNAseq Pipeline.
+#
+# Copyright © 2019 Bora Uyar <bora.uyar@mdc-berlin.de>
+#
+# This file is part of the PiGx RNAseq Pipeline.
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+# R script takes as input a BAM file and exports a coverage track
+# in bigwig format. Uses DESeq2 estimated size factors to normalize
+# the coverage tracks by size factors computed across all 
+# samples available in the sample sheet. 
+# (see DESeq2::estimateSizeFactors)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+bamFile <- args[1] # alignment file
+sampleName <- args[2] 
+size_factors_file <- args[3] #deseq size factors for all samples
+outDir <- args[4] # where to write the bigwig files
+
+#' @param cov RLE-list object 
+#' @param size_factor single numeric value corresponding 
+#' to the size factor for the sample 
+#' (see DESeq2::estimateSizeFactors)
+scale_coverage <- function(cov, size_factor) {
+  cov_scaled <- lapply(cov, function(x) {
+    S4Vectors::runValue(x) <- round(S4Vectors::runValue(x) / size_factor, 1)
+    return(x)
+  })
+  return(as(cov_scaled, "SimpleRleList"))
+}
+
+message(date()," ... Reading alignments from bam file: \n",bamFile,"\n")
+aln <- GenomicAlignments::readGAlignments(file = bamFile, index = bamFile)
+
+size_factors <- read.table(size_factors_file)
+
+message(date()," ... Getting strand-specific coverage data")
+cov_pos <- scale_coverage(cov = GenomicRanges::coverage(aln[GenomicRanges::strand(aln) == '+',]), 
+                          size_factor = size_factors[sampleName,])
+cov_neg <- scale_coverage(cov = GenomicRanges::coverage(aln[GenomicRanges::strand(aln) == '-',]), 
+                          size_factor = size_factors[sampleName,])
+
+out_pos <- file.path(outDir, paste0(sampleName, ".forward.bigwig"))
+out_neg <- file.path(outDir, paste0(sampleName, ".reverse.bigwig"))
+
+message(date(), " ... exporting bigwig files")
+
+rtracklayer::export.bw(cov_pos, con = out_pos, format = 'bw')
+rtracklayer::export.bw(cov_neg, con = out_neg, format = 'bw')
+
+message(date(), " ... Finished genome coverage processing")