« Return to Thread: automated stand alone blast with repeat masker

automated stand alone blast with repeat masker

by nisa_dar :: Rate this Message:

Reply to Author | View in Thread

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

 « Return to Thread: automated stand alone blast with repeat masker