From 14df931f3e3f950dc8c9b213c8802330ee1eb74c Mon Sep 17 00:00:00 2001
From: Georgi Tushev <georgi.tushev@brain.mpg.de>
Date: Tue, 5 Feb 2019 10:49:29 +0100
Subject: [PATCH] add genome coverage

---
 batchGenomeCoverage.pl | 43 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)
 create mode 100644 batchGenomeCoverage.pl

diff --git a/batchGenomeCoverage.pl b/batchGenomeCoverage.pl
new file mode 100644
index 0000000..1e6a1ef
--- /dev/null
+++ b/batchGenomeCoverage.pl
@@ -0,0 +1,43 @@
+#!/usr/bin/perl
+
+use warnings;
+use strict;
+use File::Basename;
+
+my $pathSource = shift;
+my $pathDest = shift;
+
+my $nodes = 1;
+my $partition = "bedtools genomecov";
+my $time = "100:00:00";
+my $ntasks = 1;
+my $cpus = 128;
+my $name = "braintest";
+
+# print header
+print "#!/bin/bash\n";
+print "\n";
+print "#SBATCH --nodes=$nodes\n";
+print "#SBATCH --partition=$partition\n";
+print "#SBATCH --time=$time\n";
+print "#SBATCH --ntasks=$ntasks\n";
+print "#SBATCH --cpus-per-task=$cpus\n";
+print "#SBATCH --job-name=$name\n";
+print "#SBATCH --error=error_\%j.out\n";
+print "#SBATCH --output=output_\%j.out\n";
+print "\n";
+print "echo \$SLURM_SUBMIT_DIR\n";
+print "echo \"Running on \`hostname\`\"\n";
+print "\n";
+
+my @fileList = glob($pathSource . "/*.bam");
+foreach my $file (@fileList) {
+
+    my $fileName = fileparse($file, ".bam");
+    my $fileOut = $pathDest . "/" . $fileName . ".gbed";
+    print "bedtools genomecov -ibam " . $file . " -bg -split | sort -k1,1 -k2,2n -k3,3n | bgzip > " . $fileOut . "\n";
+    print "tabix --zero-based --sequence 1 --begin 2 --end 3 " . $fileOut . "\n";
+}
+
+
+