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

[Jason Stajich]

Please keep this on list discussions 

Sent from my iPhone-please excuse typos

--
Jason Stajich

Begin forwarded message:

> From: José Luis Lavín <jluis.lavin at unavarra.es>
> Date: November 14, 2011 8:04:25 AM EST
> To: Jason Stajich <jason.stajich at gmail.com>
> Subject: Re: [Bioperl-l] Fwd: How to get Remote BLAST results in a single out
> 
> Hello Jason,
> 
> As answering your question:
> 
> " 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?"
> 
> A concatenation of BLAST (default format) reports should be OK, since I have a script to parse that kind of results. Anyway formats 1 or 2 will also do the trick. 
> I'll be happy to get assistance  on how to change the OUTFILE from "a query a report" to "all queries in the same report", because I don't seem to be able to do it myself after reading the module documentation.
> 
> Thanks in advance
> 
> El 14 de noviembre de 2011 12:59, Jason Stajich <jason.stajich at gmail.com> escribió:
> 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
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
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> 
> 
> -- 
> -- 
> Dr. José Luis Lavín Trueba
> 
> Dpto. de Producción Agraria
> Grupo de Genética y Microbiología
> Universidad Pública de Navarra
> 31006 Pamplona
> Navarra
> SPAIN