[Bioperl-l] searchIO parse

[Andrew Hynes]

Hi Liu,

You need to set '_READMETHOD' => 'Blast' in your @params and you can then
call methods directly on your $blast_report object.

  # Set blast params
  my @params = (
              'database' => $blast_index,
              'program'  => $blast_prog ,
              '_READMETHOD' => 'Blast'
             );

  # Create blast factory object
  my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);

  # Create seq object 
  my $input = Bio::Seq -> new ('-id' => "test_query", '-seq' => $query);

  # Kick off blast job.
  my $blast_report = $factory->blastall($input);

  # Parse the report
  my $result = $blast_report->next_result;

  while( my $hit = $result->next_hit) {
    print "Hit Name: ", $hit->name, "\n";
    print "Hit Significance: ", $hit->significance, "\n";
  }

See also
http://www.pasteur.fr/recherche/unites/sis/formation/bioperl/2eme_journee-1.
0.html#blast-parse

...... 
my @params=('program' => 'blastn', 'database' => $db);
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
my $input = Bio::Seq -> new ('-id' => "test_query", '-seq' => $query);
my $blast_report =$factory->blastall($input);
my $searchio= new Bio::SearchIO('format' => 'blast', '-file'
=>$blast_report);
......


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