automated stand alone blast with repeat masker
Hi,
I'm running a stand alone blast against my local databases by using the following code
use Bio::Seq;
use Bio::Tools::Run::StandAloneBlast;
@params = (program => 'blastn', database => 'db.fa');
$blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
$seq_obj = Bio::Seq->new(-id =>"test query", -seq =>"TTTAAATATATTTTGAAGTATAGATTATATGTT");
$report_obj = $blast_obj->blastall($seq_obj);
$result_obj = $report_obj->next_result;
print $result_obj->num_hits;
How can I include the code for repeat masker in it?
Thanks
Nisa