[Bioperl-l] Trouble using RemoteBlast.pm

[Hubert Prielinger]

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?