First I would suggest simplifying the code. You have a bunch of "if" statements that are essentially "and" conditions. Your code will work, but this introduces more levels of {} which is not good. 
if( $hsp->length('total') > 1000 ) {
      if ( $hsp->percent_identity >= 90 ) {
       if(    $hsp->score ){
        if(     $hsp->gaps ){
         if(  $hsp->expect ){
            print  "Hit= ",    $hit->name, 
                    " Length=",     $hsp->length('total'), 
                    " Score=",        $hsp->score,"\n";
            print "Gaps=",    $hsp->gaps,
                    " Expect=",        $hsp->expect,
                    " Percent_id=", $hsp->percent_identity, "\n";
            my $aln = $hsp->get_aln;
            my $alnIO = Bio::AlignIO->new(-format =>"clustalw", -file 
+=> $out);
            $alnIO->write_aln($aln);
        }
       }
      }
     }
    }

##  better is to reduce the levels of "if" by using "and" or &&
if (      ($hsp->length('total') > 1000 )   
      &&  ($hsp->percent_identity >= 90 )
      &&  ($hsp->score )
      &&  ($hsp->gaps)
      &&  ($hsp->expect)
    ) 
    {
      #do your print stuff
    }

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In my opinion when I see eight consecutive "}"'s in a row, I figure that something is wrong with the code - too many levels of indentation!

I was looking at your while loop and it is hard for me to say exactly how to make that better as there can be a lot of cases here and I am unable to run your current code without installing some modules.

Can you simplify your question?

In reply to Re: parsing blast output by Marshall
in thread parsing blast output by lomSpace

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