--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wig_extractor.pl	Mon Dec 03 03:10:23 2012 -0500
@@ -0,0 +1,143 @@
+#!/usr/bin/perl
+use Getopt::Long;
+use Cwd;
+
+my $filename;
+my $parent_dir = getcwd();
+
+my %fhs;
+my %bases_cov;
+my %bases_meth;
+my ($cov_cutoff,$cov_file, $meth_file, $context, $cov_out, $meth_out) = process_commandline();
+
+process_results_file();
+
+sub process_commandline{
+  my $cov_cutoff=1;
+  my $cov_file=0;
+  my $meth_file=0;
+  my $context="cpg,chh,chg";
+  #my $chrom_out;
+
+  # Files to extract:
+  # c -> Coverage
+  # m -> Methylation
+  # b -> Coverage + Methylation
+
+  my $files_to_extract;
+  my $command_line = GetOptions ( 'cutoff=i' => \$cov_cutoff,
+				  'e|extract=s' => \$files_to_extract,
+				  'context=s' => \$context,
+				  #'chrom=s' => \$chrom_out,
+				  'cov_out=s' => \$cov_out,
+				  'meth_out=s' => \$meth_out);
+
+
+  ### EXIT ON ERROR if there are errors with any of the supplied options
+  unless ($command_line){
+    die "Please respecify command line options\n";
+  }
+
+  ### no files provided
+  unless (@ARGV){
+    die "You need to provide a file to parse!\n";
+  }
+  $filename = $ARGV[0];
+
+  ### no files to extract specified
+  unless ($files_to_extract){
+    die "You need to specify the file you want to extract!\n";
+  }
+
+  if ($files_to_extract eq "c" or $files_to_extract eq "b"){
+		$cov_file=1;
+	}
+	if ($files_to_extract eq "m" or $files_to_extract eq "b"){
+		$meth_file=1;
+	} 
+  return ($cov_cutoff,$cov_file, $meth_file, $context, $cov_out, $meth_out);
+}
+
+sub process_results_file{
+    %fhs = ();
+    #if (defined($chrom_out)){
+    #  $chrom_out = "chr".$chrom_out;
+    #  print "\n$chrom_out\n";
+    #}
+    warn "\nNow reading in input file $filename\n\n";
+    open (IN,$filename) or die "Can't open file $filename: $!\n";
+	
+    my($dir, $output_filename, $extension) = $filename =~ m/(.*\/)(.*)(\..*)$/;
+  
+    ### OPENING OUTPUT-FILEHANDLES
+    my $wig_cov = my $wig_meth = $output_filename;
+    if ($cov_file == 1){
+    	#$wig_cov =~ s/^/Coverage_/;
+    	#$wig_cov = $dir."/".$wig_cov.".wig"; 
+	open ($fhs{wig_cov},'>',$cov_out) or die "Failed to write to $cov_out $!\n";
+	printf {$fhs{wig_cov}} ('track name="'.$output_filename.'" description="coverage per base" visibility=3 type=wiggle_0 color=50,205,50'."\n");
+    } 
+    if ($meth_file == 1){
+    	$wig_meth =~ s/^/Methylation_/;
+    	$wig_meth = $dir."/".$wig_meth.".wig";  
+	open ($fhs{wig_meth},'>',$meth_out) or die "Failed to write to $meth_out $!\n";
+	printf {$fhs{wig_meth}} ('track name="'.$output_filename.'" description="percentage methylation" visibility=3 type=wiggle_0 color=50,205,50'."\n");
+    }
+    
+   
+    while (<IN>){
+		next if $. == 1;
+	  	my ($chrom,$start,$strand,$cont,$coverage,$percentage_meth) = (split("\t"))[0,1,2,3,4,6];
+		$chrom = "\L$chrom";
+		if ("\U$chrom" !~ /CHR.*/){
+		  $chrom = "chr".$chrom;
+		}	
+	  	next if $coverage < $cov_cutoff;
+		#print "\n$chrom:$chrom_out\n";
+		next if (defined($chrom_out) and ($chrom ne $chrom_out));
+		#print "\n2\n";
+		next if not ("\U$context" =~ $cont);
+		#print "\n3\n";
+
+	  	if (defined($last_chrom) and $last_chrom ne $chrom){
+				write_files($last_chrom);
+	  	}
+			if ($cov_file == 1){
+				$bases_cov{$start}=$strand.$coverage;
+			}
+			
+			if ($meth_file == 1){
+				$bases_meth{$start}=$strand.$percentage_meth;
+			}
+	  	
+		  $last_chrom = $chrom;
+   	}
+   	write_files($last_chrom);
+}
+
+
+
+sub write_files(){
+	my ($chrom) = @_;
+	# modify chromosome name, if not starting with "chr.."
+	
+
+	if ($cov_file == 1){
+		printf {$fhs{wig_cov}} ("variableStep chrom=".$chrom." span=1\n");
+		for my $k1 (sort { $a <=> $b } keys %bases_cov){
+			printf {$fhs{wig_cov}} ("%u\t%d\n",$k1, $bases_cov{$k1});
+		}
+			%bases_cov =();
+	}
+			
+	if ($meth_file == 1){
+		printf {$fhs{wig_meth}} ("variableStep chrom=".$chrom." span=1\n");
+		for my $k1 (sort { $a <=> $b } keys %bases_meth){
+			printf {$fhs{wig_meth}} ("%u\t%.2f\n",$k1, $bases_meth{$k1});			
+		}
+		%bases_meth =();
+	}
+}
+	
+
+