[Bioperl-l] Retrieve results for an RID

[Jason Stajich]

ohh - so you're not inventing your own blast + RID system.  That is what I
took from your 1st mail.

What happens when you paste that RID into the box @ NCBI?

see below also
On Mon, 26 Jul 2004, Nurcan Mete wrote:

> 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')

These RIDs are removed because they failed.  If $rc < 0 there was an
error.  You should not be inserting these into your database.

If you'd rather just insert all the RIDs into your db initially rather
than doing this loop in the first place if what you want to do is then
retreive them later anyways.

>
> 		    $factory->remove_rid($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?

No that is all fine I guess.  Just get rid of the perl part and see what
the RID value gives you when you post it on the NCBI site.
>
>
> 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.
> > >
> > >
> > >
> > >
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> >
> > --
> > Jason Stajich
> > Duke University
> > jason at cgt.mc.duke.edu
> > _______________________________________________
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> >
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> >
>
>
>
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu