BCsplitBestRadPE2.pl

#!/usr/bin/perl

if ($#ARGV == 3) {
	$file1 = $ARGV[0];
	$file2 = $ARGV[1];
	$barcode = $ARGV[2];
	$prefix = $ARGV[3];
} else {
	die;	
}

@commas = split(/\,/, $barcode);
$barcode_length = length($commas[0]);

$x=0;
while ($x <= $#commas) {
	$hash_r1{$commas[$x]} = $prefix . "_" . $commas[$x] . "_R1.fastq";
	$hash_r2{$commas[$x]} = $prefix . "_" . $commas[$x] . "_R2.fastq";
	$filename_r1 = $hash_r1{$commas[$x]};
	$filename_r2 = $hash_r2{$commas[$x]};
	open($filename_r1, ">$filename_r1") or die;
	open($filename_r2, ">$filename_r2") or die;
	$x++;
}


open(FILE1, "<$file1") or die;
open(FILE2, "<$file2") or die;


while (<FILE1>) {

	$f1a = $_;
	$f1b = <FILE1>;
	$f1c = <FILE1>;
	$f1d = <FILE1>;

	$f2a = <FILE2>;
        $f2b = <FILE2>;
        $f2c = <FILE2>;
        $f2d = <FILE2>;
	
	$bc1 = substr($f1b,0,$barcode_length);
	$bc2 = substr($f2b,0,$barcode_length);
	
	if ($hash_r1{$bc1} ne "" && $hash_r1{$bc2} eq "")  {

		$f1b_2 = substr($f1b, $barcode_length, length($f1b));
		$f1d_2 = substr($f1d, $barcode_length, length($f1d));

		$out1 = $hash_r1{$bc1};
		$out2 = $hash_r2{$bc1};

		print $out1 $f1a . $f1b_2 . $f1c . $f1d_2;
		print $out2 $f2a . $f2b . $f2c . $f2d;

	} elsif ($hash_r1{$bc1} eq "" && $hash_r1{$bc2} ne "")  {

		$f2b_2 = substr($f2b, $barcode_length, length($f2b));
                $f2d_2 = substr($f2d, $barcode_length, length($f2d));

		$out1 = $hash_r1{$bc2};
                $out2 = $hash_r2{$bc2};

                print $out1 $f2a . $f2b_2 . $f2c . $f2d_2;
                print $out2 $f1a . $f1b . $f1c . $f1d;

	} elsif ($hash_r1{$bc1} ne "" && $hash_r1{$bc2} ne "")  {

		print "Double Barcode!\t$bc1\t$bc2\n";
	
	}

}
close FILE1; close FILE2;



$x=0;
while ($x <= $#commas) {
        close($hash_r1{$commas[$x]});
	close($hash_r2{$commas[$x]});
        $x++;
}