Furter investigation is required.

Here is the call method:

  %evals = parseFiles::getEvals();
  print Dumper \%evals;
[download]

and here is the assignment:

for(my $i = 0 ; $i<scalar @blastLine; $i++)
  {
   if ($blastLine[$i] =~ /^>/)
   {
     $counter = 0;
     $current_subject = $blastLine[$i];
     chomp ($current_subject);
     push (@subjects, $current_subject);
     $alignment->{$current_subject} = "";    
### assignment here for key value####
     $evals{$current_subject} = $blastLine[$i];
   }
    $alignment->{$current_subject} = $alignment->{$current_subject}.$b
+lastLine[$i];

   if($blastLine[$i] =~ /\bScore/)           
# check to see if the current line points to the e-value
   {
      $counter++;
      my @tempArray = split(",",$blastLine[$i]);    
# chop the line into an array for processing
      $tempArray[1] =~ s/(Expect|Expect\(2\))\s=\s//g;   #strip off an
+y digits,spaces, or = signs to get just e-value
      if($counter eq 1)
      {
### assignment here for value####
        $evals{$current_line} = $tempArray[1];
      }
   }
  }
[download]

this shows:

$VAR1 = { '>gi|19908487|gb|AF343350.1|' => '>gi|19908487|gb|AF343350.1
+|'
[download]

I'm probably missing your intent here, but I see that you:
$current_subject = $blastLine[$i];
and then you:
$evals{$current_subject} = $blastLine[$i];

This looks like it would produce a hash with matching key and value.

Yes, i see you point. A bit pointless. I think the value is modified later on though to tempArray[0]. I took out those lines though to ovoid later confusion in my code,

thanks.