BLASTN 2.2.6 [Apr-09-2003]

RID: 1064815728-21972-271666.BLASTQ3
Query= Test
         (560 letters)

No significant similarity found. For reasons why, click here.

---------------------------------------------------

-----Original Message-----
From:	Jason Stajich [mailto:jason@cgt.duhs.duke.edu]
Sent:	Mon 9/29/2003 9:32 AM
To:	010381P GOH PHUAY CHENG
Cc:	
Subject:	Re: problem connecting to remote blast

I suppose it might be because you specified an entrez query for homo
sapiens on the ecoli db - that is not going to return any hits.  remove
the entrez query part perhaps.

please post your questions to the bioperl list in the future -
bioperl-l@bioperl.org

Thanks,
-jason

On Mon, 29 Sep 2003, 010381P GOH PHUAY CHENG wrote:

> hi Jason,
> i encountered some problems running the remote blast.could u please check
for
> me wats wrong with my codes. Thanks.
>
> phuay cheng
>
> -------------------- WARNING ---------------------
> MSG: 

> INFO: [blastsrv4.REAL]: Error: Segmentation violation
> (or m
> emory usage limit was exceeded) SIGSEGV (11).
> 

> 
> BLASTN 2.2.6 [Apr-09-2003]
>
> RID: 1064796976-1676-2574126.BLASTQ3
> Query= Test
>          (560 letters)
>
> No significant similarity found. For reasons why,  "/blast/blast
> _FAQs.html#no hits">click here.

>
>
> ---------------------------------------------------
>
> #!/usr/bin/perl -w
> use Bio::SeqIO;
> use Bio::Tools::Run::RemoteBlast;
>   use strict;
>   my $prog = 'blastn';
>   my $db   = 'ecoli.nt';
>   #my $e_val= '1e-10';
>   my @params = ( '-prog' => $prog,
>          '-data' => $db,
>          '-readmethod' => 'SearchIO' );
>   my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
>
>   $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> [ORGN]';
>
>   delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
>   my $v = 1;
>
>   my $str = Bio::SeqIO->new(-file=>'test.txt' , '-format' => 'fasta' );
>   while (my $input = $str->next_seq()){
>
>     #my $r = $factory->submit_blast($input);
>     my $r = $factory->submit_blast('test.txt');
>     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
>           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";
>             }
>           }
>         }
>       }
>     }
>   }
>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu

From 010381P at nyp.edu.sg  Mon Sep 29 02:16:45 2003
From: 010381P at nyp.edu.sg (010381P GOH PHUAY CHENG)
Date: Thu Oct  2 08:21:52 2003
Subject: [Bioperl-l] problem with remote blast
Message-ID: 

hi,
i am trying to connect to the remote blast. but i encountered the following
warnings. could u pls help me.

-------------------- WARNING ---------------------
MSG: 

INFO: [blastsrv4.REAL]: Error: Segmentation violation
(or m
emory usage limit was exceeded) SIGSEGV (11).

BLASTN 2.2.6 [Apr-09-2003]

RID: 1064815996-23369-1254165.BLASTQ3
Query= Test
         (560 letters)

No significant similarity found. For reasons why, click here.

---------------------------------------------------

my codes:
#!/usr/bin/perl -w
use Bio::SeqIO;
use Bio::Tools::Run::RemoteBlast;
use strict;
  my $prog = 'blastn';
  my $db   = 'ecoli.nt';
  my $e_val= '1e-10';
  my @params = ( '-prog' => $prog,
         '-data' => $db,
          );
  my $factory = Bio::Tools::Run::RemoteBlast->new(@params);

  delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
  my $v = 1;  

  my $str = Bio::SeqIO->new(-file=>'test.txt' , '-format' => 'fasta' );
  while (my $input = $str->next_seq()){

    #my $r = $factory->submit_blast($input);
    my $r = $factory->submit_blast('test.txt');
    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
          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";
            }
          }
        }
      }
    }
  }