[Bioperl-l] Retrieve results for an RID

[Nurcan Mete]

No, I don't think I am trying to add something to
standard Blast output.

I use standard Bio::Perl 'blast_sequence' function to
blast my sequences.
In the loop section, I have one small modification: I
insert into database the request ID of the blast that
has failed to be completed by the time.

LOOP :
    while( my @rids = $factory->each_rid) {
	foreach my $rid ( @rids ) {
	    my $rc = $factory->retrieve_blast($rid);
	    if( !ref($rc) ) {
		if( $rc < 0 ) {
		    
                    # INSERT INTO TEMP_TABLE
                    # (request_id) VALUES('$rid')

		    $factory->remove_rid($rid);		    
		}
		if( $verbose ) {
		    print STDERR ".";
		}
		sleep 10;
	    } else {
		$result = $rc->next_result();
		$factory->remove_rid($rid);
		last LOOP;
	    }
	}
    }
    
    
Then, later (ie. at midnight),  I want to retrive
blast results giving this stored RID.
very simply, I use the same function code to achieve
so:

 
----------------------------------------------------------
 my @params = ( '-prog' => $prog,
		'-expect' => $e_val,
		'-readmethod' => 'SearchIO' );

    
 my $factory =
Bio::Tools::Run::RemoteBlast->new(@params);    
    
 my $rc = $factory->retrieve_blast($rid);

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

$rid: request ID stored in the database
     
I omit the following parts of original code:

my $r = $factory->submit_blast($seq);

while( my @rids = $factory->each_rid) {	
	foreach my $rid ( @rids ) {   	




so may the problem be with this omission?


I hope these details are more explanative.

Thank you.
	




--- Jason Stajich <jason at cgt.duhs.duke.edu> wrote:
> Hmm - As I said in the perlmonks post you need to
> give more information,
> i.e. a copy of the report which is failing.  Is your
> webscript adding
> things to the report which are not part of the
> standard BLAST output, etc.
> 
> -j
> On Fri, 23 Jul 2004, Nurcan Mete wrote:
> 
> >
> > I want to add some functionality to my website,
> that
> > is similar to "Retrieve results for an RID" of
> NCBI
> > blast.
> > In other words i am trying to retrieve blast
> results
> > using a particular rid.
> >
> >
> > following is the code:
> >
> >
> ----------------------------------------------------
> >
> > my @params = ( '-prog' => 'blastn',
> > 		       '-expect' => 1,
> > 		       '-readmethod' => 'SearchIO' );
> >
> >
> > my $factory =
> > Bio::Tools::Run::RemoteBlast->new(@params);
> >
> > my $rc = $factory->retrieve_blast($rid);
> >
> >
> ----------------------------------------------------
> >
> > $rid is a legitimate request ID that is passed as
> > parameter to the function.
> > retrieve_blast function returns
> > Bio::SearchIO::blast=HASH(0x2c9bf8), that
> indicates
> > the success.
> >
> > but $rc->next_result() function fails and I get
> the
> > following error.
> >
> >
> > ------------- EXCEPTION  -------------
> > MSG: no data for midline               genome
> > STACK Bio::SearchIO::blast::next_result
> >
>
/usr/perl5/site_perl/5.6.1/Bio/SearchIO/blast.pm:1151
> > STACK main::test_blast
> > /var/apache/cgi-bin/user/blast.pl:578
> > STACK toplevel
> /var/apache/cgi-bin/user/blast.cgi:65
> >
> > --------------------------------------
> >
> > How can I do this.
> >
> > Thanks.
> >
> >
> >
> >
> > __________________________________
> > Do you Yahoo!?
> > Yahoo! Mail - You care about security. So do we.
> > http://promotions.yahoo.com/new_mail
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> >
>
http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
>
http://portal.open-bio.org/mailman/listinfo/bioperl-l
> 



		
_______________________________
Do you Yahoo!?
Express yourself with Y! Messenger! Free. Download now. 
http://messenger.yahoo.com