perl - How to get status update in NCBI standalone BLAST? -

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for example, running standalone blast+ thousands of est sequences remote (ncbi) server. not getting status message 15 of 100 sequence running. possible status message that? or other way send 1 after sequence using perl scripts?
many thanks!

i suggest using bioperl (http://metacpan.org/pod/bioperl) , bio::tools::run::remoteblast module. see http://metacpan.org/pod/bio::tools::run::remoteblast , here code example give in remoteblast.pm module

 while (my $input = $str->next_seq()){     #blast sequence against database:         #alternatively,  pass in file many     #sequences rather loop through sequence 1 @ time     #remove loop starting 'while (my $input = $str->next_seq())'     #and swap 2 lines below example of that.     $r = $factory->submit_blast($input);     #my $r = $factory->submit_blast('amino.fa');      print stderr "waiting..." if( $v > 0 );     while ( @rids = $factory->each_rid ) {       foreach $rid ( @rids ) {         $rc = $factory->retrieve_blast($rid);         if( !ref($rc) ) {           if( $rc < 0 ) {             $factory->remove_rid($rid);           }           print stderr "." if ( $v > 0 );           sleep 5;         } else {           $result = $rc->next_result();           #save output           $filename = $result->query_name()."\.out";           $factory->save_output($filename);           $factory->remove_rid($rid);           print "\nquery name: ", $result->query_name(), "\n";           while ( $hit = $result->next_hit ) {             next unless ( $v > 0);             print "\thit name ", $hit->name, "\n";             while( $hsp = $hit->next_hsp ) {               print "\t\tscore ", $hsp->score, "\n";             }           }         }       }     }   }

look @ method retrieve_blast (http://metacpan.org/pod/bio::tools::run::remoteblast#retrieve_blast). return status code let know if blast job finished. let me know if have more questions , try clarify further.

paul


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