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

[Jason Stajich]

did you provide 'hmmer' as the format type?


On Mon, 26 Apr 2004, Alberto Davila wrote:

> 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";
>
>                                                                    }
>                                                             }
>                                                          }
>
>
>
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu