[Bioperl-l] Trouble using RemoteBlast.pm

[Barry Moore]

Nagesh-

Did you get this figured out?  Your script works as is on my system.
You say temp.out is empty?  What does you input sequence
(blastInput.txt) look like?

Barry

> -----Original Message-----
> From: bioperl-l-bounces at portal.open-bio.org [mailto:bioperl-l-
> bounces at portal.open-bio.org] On Behalf Of Hubert Prielinger
> Sent: Monday, January 16, 2006 2:54 PM
> To: Nagesh Chakka; bioperl-l at portal.open-bio.org
> Subject: Re: [Bioperl-l] Trouble using RemoteBlast.pm
> 
> Nagesh Chakka wrote:
> 
> >Hi All,
> >I was trying to setup a system to perform a remote blast on regular
> basis. I
> >thought this could be best achieved by using BioPerl module and came
> across
> >RemoteBlast.pm
> >I had modified the sample script "bp_remote_blast.pl" which takes a
file
> >containing single FASTA sequence as an input. Also I wanted the blast
> report
> >to be saved in a file for latter use and
> >modified the code as follows
> >I am using the latest version of Bioperl (1.5) on a Fedora platform.
>
>#######################################################################
> >print "$Bio::Root::Version::VERSION\n";
> >use Bio::Tools::Run::RemoteBlast;
> >use strict;
> >my $prog = 'blastp';
> >my $db   = 'swissprot';
> >my $e_val= '1e-10';
> >
> >my @params = ( '-prog' => $prog,
> >       '-data' => $db,
> >       '-expect' => $e_val,
> >       '-readmethod' => 'SearchIO' );
> >
> >my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
> >
> >#change a paramter
> >$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens
> >[ORGN]';
> >
> >#remove a parameter
> >delete $Bio::Tools::Run::RemoteBlast::HEADER{'FILTER'};
> >
> >my $v = 1;
> >#$v is just to turn on and off the messages
> >
> >my $r = $factory->submit_blast('blastInput.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
> >                {
> >                        print "RID $rid\n";
> >                        $factory->save_output('temp.out');
> >                        $factory->remove_rid($rid);
> >                }
> >        }
> >}
> >
>
>#######################################################################
##
> ########
> >
> >This script prints the RID and terminates immediately. Obviously the
> >output file created is empty as the program did not wait for getting
the
> >blast results from the RID.
> >Is there something I am doing wrong and what can I do for the program
to
> wait
> >until the results are ready to be printed to the output file. I could
not
> get
> >much information from the documentation and have no prior experience
with
> >Bioperl.
> >Thanks very much for  your attention.
> >Regards
> >Nageshbi
> >_______________________________________________
> >Bioperl-l mailing list
> >Bioperl-l at portal.open-bio.org
> >http://portal.open-bio.org/mailman/listinfo/bioperl-l
> >
> >
> >
> >
> hi nagesh,
> try this, should work, I had the same problem:
> 
> .......................
> .......................
> 
> else
>                 {
>                         print "RID $rid\n";
>                         $factory->save_output('temp.out');
> 
> 			my $checkinput = $factory->file;
>               		open(my $fh,"<$checkinput") or die $!;
>               		while(<$fh>){
>                 		print;
>               		}
>               		close $fh;
> 
> 
> 			$factory->remove_rid($rid);
>                 }
>         }
> }
> 
> regards
> Hubert
> 
> PS: are you using the composition based statistics parameter with your
> blast search?
> if yes, is it working?
> 
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