########
# not sure about this
my @file =();
my $html = new CGI;
my $filehandle = $html->upload('upload');
my $filename = $html->param('upload');


my $line;
my @cols;
########

# read through the file and get the sequence
sub checkFile()
{
 # print("The path name was: $file");
    print("Opening File...");
    open( FILE, "<$filehandle") or die("Error opening the file<BR>");
      
    print("File is now open");
    @file = <FILE>;
    print("<BR><BR> @file<BR><BR>");
    while($line = <FILE>)
    {
      chomp($line);
      if($line =~ /([^ACGTacgt])/) {next;}
      else
      {
        @cols = split(/\s/, $line);
        print("@cols");
      }
      close( FILE ) or die("Error closing the file<BR>");
      print("File is now closed");
    }
}