sub get_Results()
{

open( NEWACC, ">ref_files/$newRefFile" ) || die "$!";
open( NEWALIGN, ">blast_files/$newBlastFile") || die "$!";

## put list of reference accessions into a structure so we can parse i
+t...
my %refList = ();

while (<$ref_filehandle>)    # used instead of REFFILE
{
    chomp;                                # removes newline character
    my $key = $_;
  $refList{ $key } = "$_";
}

#PARSE BLAST RESULT HERE....
#read results file one line at a time
my @resultLine = <$blast_filehandle>;    # used instead of BLASTFILE
my $alignment = {};    # reference to an empty hash
my @subjects;  # reference to empty array
my $current_subject = "front_matter";
$alignment->{$current_subject} = "";

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} = $alignment->{$current_subject}.$r
+esultLine[ $i ];
}

my @elements;

foreach my $z (@subjects)
{
    chomp $z;
    @elements = split('\|', $z);

    if ( ! defined $elements[ 3 ] )
  {
        print ("Parsing Error<BR>");
        print ("Line $z");
    }
    ##### PROBLEM LIES HERE WITH IF STATEMENT
    if (defined $elements[3] &&  defined $refList{$elements[3]} )
    {
        print ("Already Present in file");
    }
    else
    {
        print "No match in reference file";
        print (NEWALIGN $alignment->{$z}."\n");
        print (NEWACC $elements[3]."\n");
    }
}

#close files
close NEWALIGN;
close NEWACC;
}
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