--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyCRAC/pyBarcodeFilter.pl	Tue Jun 18 09:11:00 2013 -0400
@@ -0,0 +1,71 @@
+#!/usr/bin/perl -w
+use strict;
+use Getopt::Long;
+
+my %opt;
+
+
+GetOptions(\%opt, "f=s", "b=s", "out=s", "output_path=s","id=s","m=i", "file_type=s", "both", "r=s", "version", "i");
+
+my $cmnd;
+
+if (exists $opt{version}){
+	$cmnd = "python /usr/local/bin/pyBarcodeFilter.py --version";
+}
+else{
+	$cmnd = "python /usr/local/bin/pyBarcodeFilter.py -f $opt{f} -b $opt{b} -m $opt{m} --file_type $opt{file_type}";
+
+	if(defined $opt{r}){
+
+	$cmnd.= " -r $opt{r}";
+
+		if(exists $opt{both}){
+			$cmnd .= " --both";
+		}
+	}
+
+	if(exists $opt{i}){
+		$cmnd .= " -i";
+	}
+}
+
+# Create the output directory (for the multiple output files)
+my $output_path = $opt{output_path};
+
+system $cmnd;
+
+open(BC,$opt{b}) || die "Cannot open barcode file";
+my %bc;
+while(my $line = <BC>){
+	chomp($line);
+	my ($barcode,$sample) = (split(/\t/,$line))[0,1];
+	$bc{$barcode}=$sample;
+}
+
+system "mv barcode_statistics.txt $opt{out}";
+
+my $ft = lc($opt{file_type});
+
+foreach my $key(keys %bc){
+	my @split = (split(/\//,$opt{f}));
+	my $l = @split;
+	my $output = $split[$l-1];
+	$output = (split(/\./,$output))[0];
+	$output = "$output"."_"."$key"."_"."$bc{$key}"."."."$ft";
+	my $rename = "$output_path/primary_$opt{id}_$bc{$key}-1"."_visible_"."$ft";
+	system "mv $output $rename"; 
+
+	if(defined $opt{r}){
+		my @split2 = (split(/\//,$opt{r}));
+		$l = @split2;
+		$output = $split2[$l-1];
+		$output = (split(/\./,$output))[0];
+		$output = "$output"."_"."$key"."_"."$bc{$key}"."."."$ft";
+		$rename = "$output_path/primary_$opt{id}_$bc{$key}-2"."_visible_"."$ft";
+		system "mv $output $rename"; 
+	}
+}
+
+
+close BC;
+