[Bioperl-l] Fwd: How to get Remote BLAST results in a single out

[Jason Stajich]

if you want to do a bunch of BLASTs remotely on the cmdline you should also just use the NCBI's blastcl3 tool (not sure if there is a BLAST+ equivalent). This might be faster to do and easier since you need to learn the programming part too.

If you want to do this within this code I guess the question is what format you want the data in - a BLAST report or something more like a table?  

On Nov 14, 2011, at 6:14 AM, José Luis Lavín wrote:

> Hello everybody,
> 
> I've been using  "Bio::Tools::Run::RemoteBlast" for a time and it has
> worked fine for me. Now I need to perform a multiple BLAST search, but this
> time I'd just like to get all the BLAST results in a single out file
> instead of having each sequence's report written individually. I've read
> the documentation of the module, but due to my short
> experience/understanding on complex modules as this one seems to be I can't
> figure out where to change the script to achieve my previously mentioned
> aim.
> Here I post the script I've been using (it's basically the one posted on
> the module cookbook).
> 
> #!/c:/Perl -w
> use Bio::Tools::Run::RemoteBlast;
> use Bio::SearchIO;
> use Data::Dumper;
> 
> #Here i set the parameters for blast
> print "Enter your BLAST choice (blastn, blastp, blastx, tblastn,
> tblastx):\n";
> my $blst = <STDIN>;
> my $prog = "$blst";
> print "Enter a database to search (nr, refseq_protein, swissprot, pat, pdb,
> env_nr):\n";
> my $dtb = <STDIN>;
> $db = "$dtb";
> print "Enter your cutt off score (1e-n):\n";
> my $cut = <STDIN>;
> my $e_val = "$cut";
> 
> my @params = ( '-prog' => $prog,
>         '-data' => $db,
>         '-expect' => $e_val,
>         '-readmethod' => 'SearchIO' );
> 
> my $remoteBlast = Bio::Tools::Run::RemoteBlast->new(@params);
> 
> 
> #Select the file and make the blast.
> print "Enter your FASTA file:\n";
> chomp(my $infile = <STDIN>);
> my $r = $remoteBlast->submit_blast($infile);
>  my $v = 1;
> 
>    print STDERR "waiting..." if( $v > 0 );  ########  WAIT FOR THE RESULTS
> TO RETURN!!!!!
>    while ( my @rids = $remoteBlast->each_rid ) {
>      foreach my $rid ( @rids ) {
>        my $rc = $remoteBlast->retrieve_blast($rid);
>        if( !ref($rc) ) {
>          if( $rc < 0 ) {
>            $remoteBlast->remove_rid($rid);
>          }
>          print STDERR "." if ( $v > 0 );
>          sleep 5;
>        } else {
>          my $result = $rc->next_result();
>          #save the output
>          my $filename =
> $result->query_name()."\.out";##################open SALIDA,
> '>>'."$^T"."Report"."\.out";
>          $remoteBlast->save_output($filename);#############
>          $remoteBlast->remove_rid($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";
>            }
>          }
>        }
>      }
>    }
> 
> 
> May any of you please explain me how to solve my question?
> 
> Thanks in advence
> 
> With best wishes
> 
> -- 
> -- 
> Dr. José Luis Lavín Trueba
> 
> Dpto. de Producción Agraria
> Grupo de Genética y Microbiología
> Universidad Pública de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
> 
> 
> 
> -- 
> -- 
> Dr. José Luis Lavín Trueba
> 
> Dpto. de Producción Agraria
> Grupo de Genética y Microbiología
> Universidad Pública de Navarra
> 31006 Pamplona
> Navarra
> SPAIN
> 
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