some variables declared before the method calls and the correct syntax for a CGI script.
###############################################################################
sub get_Input()
{
  $html = new CGI;           # create a new instance of CGI to upload file
  $blastFile = $html->param('blast_Upload');   # upload file
  $refFile = $html->param('ref_Upload');   # upload file
  $blastSeq = param("blast_Seq");
  
  chomp($refFile);
  @dir = split(/\\/, $refFile);
  pop(@dir);
  
  $pathName =  join('\\', @dir);

  print("<BR>$pathName is the location files will be saved to<BR>");
  print("<BR>$blastFile<BR>");
  print("<BR>$refFile<BR>");
}


###############################################################################
sub get_Results()
{

#my $referenceFile;
#my $blastFile;

#if using this WITHOUT an reference file as input, cmdline must be as follows
# --blastresult result.txt --reffile file.txt (even if it's an empty file)

#GetOptions( "blastresult=s" => \$blastFile, "reffile=s" => \$refFile);

 my $ref_File = "<" . $refFile;
 my $blast_File = "<" . $blastFile;

print("<BR>$blast_File<BR>");
print("<BR>$ref_File<BR>");

## open file handles.############## PROBLEM HERE ##########
open( BLAST_FILE, $blast_File ) || die "$!";
open( REF_FILE, $ref_File ) || die "$!";
print("Blast File Opened<BR>");
print("Reference File Opened<BR>");

## output files - open them
my $newRefFile = "$pathName\\newRefFile.txt";
my $newBlastFile = "$pathName\\newBlastFile.txt";

open( NEW_ACC, ">$newRefFile" ) || die "$!";
open( NEW_ALIGN, ">$newBlastFile") || die "$!";
print("New files created<BR>");


## put list of reference accessions into a structure so we can parse it...
my $refList = {};	# reference to empty hash

while (<REF_FILE>)
{
	chomp;									# removes newline character
	$refList->{$_} = "";	# $_ is whatever line is currently open, thus creating a hash with key = accession, value = " "(.: defined)
}


#PARSE BLAST RESULT HERE....
#read results file one line at a time

my @resultLine = <BLAST_FILE>;
my $alignment = {};	# reference to an empty hash
my @subjects = [];  # reference to empty array
my $current_subject = "front_matter";
$alignment->{$current_subject} = "";

#so I produce a hash with key = >gi line of report and value = all lines after until next >gi

for (my $i = 0 ; $i<scalar @resultLine; $i++)
{
	if ($resultLine[$i] =~ /^>/)
	{
		$current_subject = $resultLine[ $i ];
		chomp ($current_subject);
		push (@subjects, $current_subject);
		$alignment->{$current_subject} = "";	#$alignment->{$current_subject} means give value of $alignment when $current_subject is the key
	}

	$alignment->{$current_subject} = $alignment->{$current_subject} . $resultLine[ $i ];
}

my @elements;

foreach my $z (@subjects)
{
	chomp $z;
	print "$z\n";
	@elements = split('\|', $z);
	if ( ! defined $elements[ 3 ] )
  {
		print "<BR>Parsing Error<BR>";
		print "<BR>Line $z<BR>";
	}

	if (defined $elements[ 3 ] && defined $refList->{$elements[3]})
	{
		print "<Br>Match<BR>";
	}

	else
	{
		print "<BR>No match<BR>";
		print NEW_ALIGN $alignment->{$z} . "<BR>";
		print NEW_ACC $elements[3]."<BR>";
		print  $alignment->{$z} . "<BR>";
		print  $elements[3]."<BR>";
	}
}

#close files
close REF_FILE;
close BLAST_FILE;
close NEW_ALIGN;
close NEW_ACC;
}