How to get status update in NCBI standalone BLAST?

Question

For example, I am running standalone Blast+ for thousands of EST sequences with remote (NCBI) server. I am not getting any status message like 15 of 100 sequence is running. Is it possible to get any status message like that? or any other way to send one after another sequence using perl scripts?
Many thanks!

Answer 1

I suggest using Bioperl (http://metacpan.org/pod/BioPerl) and the Bio::Tools::Run::RemoteBlast module. See http://metacpan.org/pod/Bio::Tools::Run::RemoteBlast and here is the code example they give in the RemoteBlast.pm module

 while (my $input = $str->next_seq()){
    #Blast a sequence against a database:    
    #Alternatively, you could  pass in a file with many
    #sequences rather than loop through sequence one at a time
    #Remove the loop starting 'while (my $input = $str->next_seq())'
    #and swap the two lines below for an example of that.
    my $r = $factory->submit_blast($input);
    #my $r = $factory->submit_blast('amino.fa');

    print STDERR "waiting..." if( $v > 0 );
    while ( my @rids = $factory->each_rid ) {
      foreach my $rid ( @rids ) {
        my $rc = $factory->retrieve_blast($rid);
        if( !ref($rc) ) {
          if( $rc < 0 ) {
            $factory->remove_rid($rid);
          }
          print STDERR "." if ( $v > 0 );
          sleep 5;
        } else {
          my $result = $rc->next_result();
          #save the output
          my $filename = $result->query_name()."\.out";
          $factory->save_output($filename);
          $factory->remove_rid($rid);
          print "\nQuery Name: ", $result->query_name(), "\n";
          while ( my $hit = $result->next_hit ) {
            next unless ( $v > 0);
            print "\thit name is ", $hit->name, "\n";
            while( my $hsp = $hit->next_hsp ) {
              print "\t\tscore is ", $hsp->score, "\n";
            }
          }
        }
      }
    }
  }

Look at the method retrieve_blast (http://metacpan.org/pod/Bio::Tools::Run::RemoteBlast#retrieve_blast). It will return a status code to let you know if the blast job is finished. Let me know if you have more questions and I will try to clarify further.

Paul