Many apologies in advance for the obfuscation...

#!/opt/local/bin/perl -w
open(STDERR, ">errors.log") || die "cannot create error log";

$dir = `pwd`;
chomp $dir;
if ($dir =~ m/(^.*)(GQ.*)/) {
        $path = $1;
        $lib = $2;
        };
chop $path;
$xpath = "$path/ProjectSpecificInfo/";
print "working from $dir\n";
print "library is $lib\n";
opendir (DIR, ".") || die "cannot read from current dir";
open (XREF, "<$xpath$lib.OUT") || die "cannot open cross-ref file $xpa
+th$lib.OUT";
%XREF = ();
while (<XREF>) {
    ($SeqID, $MNid) = (split /\t/, $_)[0,1];
    $XREF{$SeqID} = $MNid;
    };
`phred -pd phd_dir *.gz`;
`phran -q $phran_cut phd_dir/*.phd.1`;
`mv $dir/phd_dir/*.raw $dir/phd_dir/phran_dir/`;
print "raw files moved to phran, now sorting\n";
while ($sequence = readdir (DIR)) {
    if ( $sequence =~ /MN/ ) {
      if ( $sequence =~ /(^.*)(\.gz)/ ) {
        $sequence = $1;
      };
        if (exists $XREF{$sequence}) {
          $seqID = $XREF{$sequence};
          if ($seqID =~ TB) {
            `mv $dir/phd_dir/phran_dir/$sequence.raw $dir/phd_dir/phra
+n_dir/3prime/`;
            } else {
            `mv $dir/phd_dir/phran_dir/$sequence.raw $dir/phd_dir/phra
+n_dir/5prime/`;
              };
        };
    };
      };

                  $threeprimedir = "$dir/phd_dir/phran_dir/3prime";
                  $fiveprimedir = "$dir/phd_dir/phran_dir/5prime";
                  @primes = ($threeprimedir, $fiveprimedir);
                  foreach $vfdir ( @primes ) {
            $pid = fork and next;
            &VF4($line);
            print "Completed $dir\n";
          };
print "processing complete for $dir\n";
                  
$dir/phd_dir/phran_dir/vf_dir/`;
sub finish {
                  chdir "$dir/phd_dir/phran_dir/vf_dir/";
          print "Running artifact filter\n";
          `af  *.seq > afresults.log`;
          `mv *qc $dir/phd_dir/phran_dir/vf_dir/af_dir/`;
          `mv afresults.log $dir/phd_dir/phran_dir/vf_dir/af_dir/`;
          `mv *.af.out $dir/phd_dir/phran_dir/vf_dir/af_dir/`;
          `mv $dir/phd_dir/phran_dir/vf_dir/*.raw $dir/phd_dir/phran_d
+ir/`;
        };

sub VF4($) {
  if ($vfdir =~ /3prime/) {
    chdir "$dir/phd_dir/phran_dir/3prime";
    `gstVF4 -o $vffile3 *.raw > 3primevf.log`;
    print "finished Running VF4 in 3prime\n";
    `mv $dir/phd_dir/phran_dir/3prime/* $dir/phd_dir/phran_dir/vf_dir/
+`;
    chdir "..";
    `rm $vfdir`;
    #&finish;
  }elsif ($vfdir =~ /5prime/) {
    chdir "$dir/phd_dir/phran_dir/5prime";
    `gstVF4 -o $vffile5 *.raw > 5primevf.log`;
    print "finished Running VF4 in 5prime\n";
    `mv $dir/phd_dir/phran_dir/5prime/* $dir/phd_dir/phran_dir/vf_dir/
+`;
    chdir "..";
    `rm $vfdir`;
    #&finish;
  };
&finish;
};
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