BarcodeSplitListBestRadPairedEnd.pl

#!/usr/bin/perl

### Author: Mike Miller

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

@commas = split(/\,/, $barcode);
$barcode_length = length($commas[0]); #telling how long the barcodes are as indicated in the .sh file

#this creates all of the files named after the barcodes.
$x=0;
while ($x <= $#commas) {
        $hash_r1{$commas[$x]} = $prefix . "_RA_" . $commas[$x] . ".fastq";
        $hash_r2{$commas[$x]} = $prefix . "_RB_" . $commas[$x] . ".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, "gunzip -dc <$file1 |") or die;
open(FILE2, "gunzip -dc <$file2 |") or die;
my $z = new IO::Compress::Gzip $output or die "IO::Compress::Gzip failed: $GzipError\n";


while (<FILE1>) {

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

        $f2a = <FILE2>;
        $f2b = <FILE2>;
        $f2c = <FILE2>;
        $f2d = <FILE2>;

        #substring returns a string from the frist argument. Second argument tells how far from 
                #the left side of the arguement to start. 
                #3rd argument limits the size of the substring that is returned.
        #so this is looking at the beginning of each forward and reverse read and pulling out
                #the bases that  contain the barcode and the cut site. Only print if match the barcode specified.
        $bc1 = substr($f1b,0,$barcode_length);
        $bc2 = substr($f2b,0,$barcode_length);

        #ne means not equal. 
        #the && is making sure both statements are true.
        #the following loop checks first bc1 for the barcode, then barcode 2.
        #last, checks both and prints if they both contain barcode, which is wrong.
        #this is also what puts them in the right orientation.
        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};

                $z-> print $out1 $f1a . $f1b_2 . $f1c . $f1d_2;
                $z-> 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};

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

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

                $z-> print "Double Barcode!\t$bc1\t$bc2\n";

        }

}
close FILE1; close FILE2;



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