#! usr/local/bin/perl 

use Cwd; 

print STDOUT "Please enter the name and location of the directory to parse\:\n";
$directory=<STDIN>;
chomp $directory;

open (OUTPUTFILE,">junk.txt"); 

opendir (DIR, "$directory") or die "Failed to open directory: $!";
@filename=readdir(DIR);
@trash=splice(@filename, 0,2);
@genius=@filename;

sub get_signal {
   while (@filename) {
      $file=shift @filename;
      @final_data='';
      use Cwd 'chdir';
      chdir "./data";
      open (FILE, "$file") or die;
      @data=<FILE>;
      $spliced_data=splice(@data, 1, 14);
      foreach (@data) {
         ($a, $b, $c, $d, $e, $f)=split(/\t/);
         push(@final_data, "$d\n");} 
      %hash={"$file"=>@final_data}; #this hash assignment +doesn't work
      close (FILE);
   }
   @values=values(%hash);
   return @values;
} 

sub get_targets {
   $target=shift @genius;
   use Cwd 'chdir';
   chdir "./data";
   open (FL, "$target") or die;
   @info=<FL>;
   $excess=splice(@info, 1, 14);
   foreach (@info) {
      ($z, $x, $w, $y, $u, $v)=split(/\t/);
      push(@targets, "$z\n");} 
   close (FL);
   return @targets;
}

@column=get_targets;
@next_columns=get_signal;

for ($i=0;$i<=scalar(@next_columns);$i++) {
   @$i=@next_columns[$i];}  #my attempt at assigning a +unique variable, which doesn't work.

print @next_columns;
print OUTPUTFILE "@final_data";
close OUTPUTFILE;
exit;