[Bioperl-l] Remote Blast Execution

[Chris Fields]

You need to update to the latest code (bioperl-live) from CVS.  BLAST
parsing using RemoteBlast is broken in all the latest releases.  

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Prabu R
> Sent: Monday, July 24, 2006 10:40 AM
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Remote Blast Execution
> 
> Dear All!
> 
> I am trying to run Remote Blast using Bio::Tools::Run::RemoteBlast.
> 
> I am not able to get the blast result.
> Upto my knowledge, the Bio::SearchIO::blast hash object does not returns
> any
> result.
> 
> 
> Secondly, I tried 'remote_blast.pl ' a program from CPAN bioperl
> 1.5release.
> 
> Command:
>  perl bp_remote_blast.pl -p blastn -d est_mouse -e 1e-5 -i
> /home/prabucn/Blast/mm_test1.fa
> 
> Error Message:
> 
> retrieving blasts..
> 
> -------------------- WARNING ---------------------
> MSG: Possible error (1) while parsing BLAST report!
> ---------------------------------------------------
> 
> Please help.
> 
> Thanks,
> R. Prabu.
> 
> 
> Please look into my test program.
> --------------------------------------------------------------------------
> --------------------
> use Bio::Tools::Run::RemoteBlast;
>   use strict;
>   use Bio::SeqIO;
>   use Bio::SearchIO;
> 
>  my $prog = 'blastn';
>   my $db   = 'est';
>   my $e_val= '1e-10';
> 
>   my @params = ( '-prog' => $prog,
>          '-data' => $db,
>          '-expect' => $e_val,
>          '-readmethod' => 'SearchIO' );
> 
>   my $factory = Bio::Tools::Run::RemoteBlast->new(@params) || die "Cant
> do";
> 
>    my $v = 1;
> 
>   my $str = Bio::SeqIO->new(-file=>'mm_test2.txt' , '-format' => 'fasta'
> );
> 
>   while (my $input = $str->next_seq()){
>      my $r = $factory->submit_blast($input);
> 
>     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 ( $v > 0 );
>           sleep 5;
>         } else {
>           print "$rc\n";
>           my $result = $rc->next_result();
>            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";
>             }
>           }
>         }
>       }
>     }
>   }
> --------------------------------------------------------------------------
> --------------------
> 
> --
> "Every noble work is at first impossible."
> - Thomas Carlyle
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l