HOWTO:SearchIO/Using

Here's example code which processes a BLAST report, then iterates through the generated objects, finding all the hits where the HSPs are greater than 50 residues and the percent identity is less than 75 percent. This code demonstrates that a result, in this case from a BLAST report, contains one or more hits, and a hit contains one or more HSPs.

use strict;
use Bio::SearchIO; 
my $in = new Bio::SearchIO(-format => 'blast', 
                           -file   => 'report.bls');
while( my $result = $in->next_result ) {
  ## $result is a Bio::Search::Result::ResultI compliant object
  while( my $hit = $result->next_hit ) {
    ## $hit is a Bio::Search::Hit::HitI compliant object
    while( my $hsp = $hit->next_hsp ) {
      ## $hsp is a Bio::Search::HSP::HSPI compliant object
      if( $hsp->length('total') > 50 ) {
        if ( $hsp->percent_identity >= 75 ) {
          print "Query=",   $result->query_name,
            " Hit=",        $hit->name,
            " Length=",     $hsp->length('total'),
            " Percent_id=", $hsp->percent_identity, "\n";
        }
      }
    }  
  }
}

The example above shows just a few of the many methods available in Bio::SearchIO system.