[Bioperl-l] Parsing "hmmsearch" results - help

[Alberto Davila]

Hi all,

I am trying to write a script to parse the "hmmsearch" results but not
sure I am using the appropriate code (eg "$hit->bits"). The code I am
listing below work ok parsing blast results but not "hmmsearch"
results... any tips ?

Thanks, Alberto


    use strict;
    use Bio::SearchIO;


	
             		while( my $hsp = $hit->next_hsp ) {
	        	$albhsp ++;

                   		if( $hsp->length('total') >= $inlength ) {
	  
	             		$alblength++;
                  
		  		if ( $hit->significance <= $inevalue ) {
          
	                	$albsignificance++;

                     	print PARSEDFILE $result->query_name,"@", 
                                         $result->query_description,"@",
	     		       		 $result->query_length, "@",
			       		 $hit->description, "@",
			       		 $hit->accession, "@",
                                         $hit->bits, "@",
 			       		 $hit->significance, "@", 
			       		 $hsp->num_identical, "@",
                                         $hsp->num_conserved,"@",  
                                         $hsp->start('query'),"@",  
                                         $hsp->end('query'),"@",
                                         $hsp->start('hit'),"@",
                                         $hsp->end('hit'),"@\n";

                        print FASTAFILE  "> ", $hit->description,"\n",
			                       $hsp->hit_string,"\n";
                                         
                                                                   }
                                                            }
                                                         }