[Bioperl-l] Trouble using RemoteBlast.pm

[Nagesh Chakka]

Bi  Barry,
With the help of Hubert, I further modified the script but still have the same 
problem. The problem is that from the point of submitting the blast query, 
the script does not wait until the blast results are ready  for retrieval and 
event of submission is immediately followed by retrieving and saving the 
output. Since the results will not be ready (about a sec) this fast, the 
output created is blank. I am able to retrieve the results online using the 
RID which I am making the script to print.
So  my main problem is making the program to wait after submitting the result. 
My input file has a single fasta sequence which I have pasted below.
Its interesting to note that the script works on your system. Is it creating 
an output file with the blast report?
Thanks very much for your attention. 
Regards
Nagesh

blastInput.txt
>MusDpl
MKNRLGTWWVAILCMLLASHLSTVKARGIKHRFKWNRKVLPSSGGQITEARVAENRPGAFIKQGRKLDIDFGAEGNRYYA
ANYWQFPDGIYYEGCSEANVTKEMLVTSCVNATQAANQAEFSREKQDSKLHQRVLWRLIKEICSAKHCDFWLERGAAL
RVAVDQPAMVCLLGFVWFIVK

On Wednesday 18 January 2006 05:34, Barry Moore wrote:
> 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?
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/bioperl-l