[Bioperl-l] Regarding Organism based search in Remote blast

[Chris Fields]

Roopa,

At one point a couple of parameters differed between NCBI's web interface and our RemoteBlast-based BLAST interface to URLAPI (this should be indicated in your BLAST reports).  See here:

http://thread.gmane.org/gmane.comp.lang.perl.bio.general/14155

Also, are the returned hits specific for the genome?  You shoudl double-check; in some cases you have to set both HEADER and RETRIEVALHEADER to get the expected results (not sure why):

http://article.gmane.org/gmane.comp.lang.perl.bio.general/18737/match=remoteblast+ncbi

chris 
 
On Dec 4, 2009, at 7:57 AM, Roopa Raghuveer wrote:

> Hello all,
> 
> I am working on Remote blast.Here,I am trying to get 2 parameters into the
> remote blast code.They are
> 
> 1.The input sequence that has to be sent to blast
> 
> 2.Organism (The organism which has to be searched for ex:-Trypanasoma brucei
> etc.,)
> 
> When I tried to take the organism parameter as an input from the
> user,through a web page,the Remote blast was not giving any results i.e., it
> says that there are no alignments found.
> 
> But,when I hard coded the organism in the code,it gives me the results i.e.,
> 3hits.
> 
> I could not understand this problem.Could any body please help me in this
> regard?
> 
> My code is
> 
> sub blastcode
> {
> 
> $input1= $_[0];
> 
> $organ= $_[1];
> 
> open(NUC,'>',$nuc);
> print NUC $input1;
> close(NUC);
> 
> my $prog = 'blastn';
> my $db   = 'refseq_rna';
> my $e_val= '1e-10';
> my $organism= $organ;
> 
> $gb = new Bio::DB::GenBank;
> 
> my @params = ( '-prog' => $prog,
>         '-data' => $db,
>         '-expect' => $e_val,
>         '-readmethod' => 'SearchIO',
>         '-Organism'   => $organism );
> 
>             open(OUTFILE,'>',$debugfile);
>               print OUTFILE @params;
>              close(OUTFILE);
> 
> 
> my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> 
>  #change a paramter
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$organism[ORGN]';
> #change a paramter
> # $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = '$input2[ORGN]';
> 
>  my $v = 1;
>  #$v is just to turn on and off the messages
> 
> my $str = Bio::SeqIO->new(-file => $nuc , '-format' => 'fasta' ,
> '-Organism' => $organism );
> 
> 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
>        $blastdebugfile = $serverpath."/blastdebug_".time().".txt";
> 
>      #    open(BLASTDEBUGFILE,'>',$debugfile);
>       #   print BLASTDEBUGFILE $result->next_hit();
>        #  close(BLASTDEBUGFILE);
> 
>        my $filename =
> $serverpath."/blastdata_".time().$result->query_name()."\.out";
> 
>         # open(DEBUGFILE,'>',$debugfile);
>         # open(new,'>',$filename);
>         # @arra=<new>;
>         # print DEBUGFILE @arra;
>         # close(DEBUGFILE);
>         # close(new);
> $factory->save_output($filename);
> 
>       # open(BLASTDEBUGFILE,'>',$debugfile);
>       # print BLASTDEBUGFILE  "Hello $rid";
>       # close(BLASTDEBUGFILE);
> 
>       $factory->remove_rid($rid);
> 
>       open(BLASTDEBUGFILE,'>',$blastdebugfile);
>       print BLASTDEBUGFILE  $organism;
>        close(BLASTDEBUGFILE);
> 
>    # open(OUTFILE,'>',$outfile);
>    # print OUTFILE "Test2 $result->database_name()";
>    # close(OUTFILE);
> 
> #$hit = $result->next_hit;
> #open(new,'>',$debugfile);
> #print $hit;
> #close(new);
> 
>   while ( my $hit = $result->next_hit ) {
> 
>            next unless ( $v > 0);
> 
>          #     open(OUTFILE,'>',$debugfile);
>           #    print OUTFILE "$hit in while hits";
>            #  close(OUTFILE);
> 
>       my $sequ = $gb->get_Seq_by_version($hit->name);
>           my $dna = $sequ->seq();        # get the sequence as a string
>                  push(@seqs,$dna);
>          }
>        }
>      }
>    }
>  }
> 
>  #open(OUTFILE,'>',$debugfile);
>  #print OUTFILE $seqs[0];
>  #close(OUTFILE);
> 
> return(@seqs);
> }
> 
> Regards,
> Roopa.
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