--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/methylation_analysis/methylation_extractor_wrapper.pl	Mon Dec 03 18:26:25 2012 -0500
@@ -0,0 +1,106 @@
+use strict;
+use warnings;
+use File::Basename; 
+use Cwd;
+use File::Path qw(make_path remove_tree);
+die qq(
+Bad numbr of inputs
+
+) if(!@ARGV);
+
+my @bam_list_entries;
+
+my $player_options = "";
+my $bam_file;
+my $ending;
+my $genome;
+my $summary ;
+my $output;
+
+foreach my $input (@ARGV) 
+{
+	my @tmp = split "::", $input;
+	if($tmp[0] eq "GENOME") 
+	{
+		$genome=$tmp[1];	
+	} 
+	elsif($tmp[0] eq "OPTION") 
+	{
+		$player_options = "$player_options ${tmp[1]}";
+	} 
+	elsif($tmp[0] eq "ENDING") 
+	{
+		$ending = $tmp[1];
+	} 
+        elsif($tmp[0] eq "BAMFILE") 
+	{
+		$bam_file = $tmp[1];
+	}
+	elsif($tmp[0] eq "SUMMARY") 
+	{
+		$summary = $tmp[1];
+	} 
+	elsif($tmp[0] eq "OUTPUT") 
+	{
+		$output = $tmp[1];
+	}
+        else 
+	{
+		die("Unknown Input: $input\n");
+	}
+}
+
+
+my $working_dir = cwd();
+
+#convert bam to sam
+my $sam_file = "$working_dir/coverted.sam";
+system("samtools view -h $bam_file > $sam_file");
+
+#run bismark 
+
+system ("bismark_methylation_extractor $ending $player_options --genome_folder $genome $sam_file > $summary 2>&1");
+
+move_files($working_dir);
+
+sub move_files
+{
+	my $name;
+	my $suffix;
+	my $path;
+	my $local_dir = $_[0];
+	opendir(DIR, $local_dir);
+	#print ("Openning: $local_dir\n");
+	my @FILES= readdir(DIR); 
+	closedir(DIR);
+	foreach my $file (@FILES) 
+	{
+		if ($file eq "." || $file eq "..")
+		{
+			#print ("./ or ../ skipped\n");
+		}
+		elsif (-d "$local_dir/$file")
+		{
+			#print ("moving to: $local_dir/$file\n");
+			move_files("$local_dir/$file");
+		}
+		elsif (-f "$local_dir/$file")
+		{
+			($name,$path,$suffix) = fileparse($file,qr"\.[^.]*$");
+			if ($suffix eq ".bedGraph")
+			{
+				system ("mv $local_dir/$file $output");
+			}
+		}
+		else
+		{
+			die("Unrecognized file generated: $file\n");
+		}
+		
+	}
+}
+
+
+
+
+