[Bioperl-l] remoteblast result in text format

[Damien Mattei]

Hello Mathieu,

sorry to haven't try your code earlier.
I try to use your save_output feature , but i can't understand what is 
the parseBlastObject() function ?

here is the code:
my $factory = Bio::Tools::Run::RemoteBlast->new();
	$Bio::Tools::Run::RemoteBlast::HEADER{'PROGRAM'} = 'blastn';
	$Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} = $blastdb;
	$Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = $evalue;
	#$Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'PAM30';
	#$Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '9 1';
	#$Bio::Tools::Run::RemoteBlast::HEADER{'WORD_SIZE'} = '2';
	#$Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'on';
	#$Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens 
[ORGN]';
         #Have to request the blast with the right amount of alignments,
	$Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENTS'} = $alignv;
	$Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = $descv;
         #and then retrieve it that way as well
	$Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'ALIGNMENTS'} = $alignv;
	$Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'DESCRIPTIONS'} = $descv;
	$Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'FORMAT_TYPE'} = 'Text';

	my $r = $factory->submit_blast($seq);
	print STDERR "waiting..." if( $r > 0 );
	while ( my @rids = $factory->each_rid ) {
	    foreach my $rid ( @rids ) {
		my $rc = $factory->retrieve_blast($rid);
		if( !ref($rc) ) {
		    if( $rc < 0 ) {
			#This is an error condition, should be a warning or something?
			$factory->remove_rid($rid);
		    }
		    print STDERR "." if ( $r > 0 );
		    sleep 5;
		} else {
		    print "Parsing $rid\n";
		    my $filename = parseBlastObject($rc);
		    $factory->save_output($rid, $filename);
		    $factory->remove_rid($rid);
		}
	    }
	}
	$factory->DESTROY;
     }

and the error i get:
waiting.........Parsing 1036349441-07089-15192
Tk::Error: Undefined subroutine &main::parseBlastObject called at 
./genmap.pl line 2326.

what's in parseBlastObject , where this subroutine belongs from? 
external code?

Thanks for your help.

Damien

Wiepert, Mathieu wrote:
> Hi,
> 
> I am not quite sure what you mean by this request.  Are you saying that you want to get the raw blast output?  If so, I can send you a modified RemoteBlast file that you can try.  I have been using it for about a week, testing it before I commit it to Bioperl.  
> 
> It is invoked like
> 
> $factory->save_output($rid, $filename);
> 
> Here is a sample script, assuming that you pass in a sequence file.  The parameters set are the same as from the short nearly exact protein match blast page at NCBI, filtered for Homo Sapiens:
> 
> my $factory = Bio::Tools::Run::RemoteBlast->new();
> $Bio::Tools::Run::RemoteBlast::HEADER{'PROGRAM'} = 'blastp';
> $Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} = 'nr';
> $Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '200000';
> $Bio::Tools::Run::RemoteBlast::HEADER{'MATRIX_NAME'} = 'PAM30';
> $Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '9 1';
> $Bio::Tools::Run::RemoteBlast::HEADER{'WORD_SIZE'} = '2';
> $Bio::Tools::Run::RemoteBlast::HEADER{'NCBI_GI'} = 'on';
> $Bio::Tools::Run::RemoteBlast::HEADER{'ENTREZ_QUERY'} = 'Homo sapiens [ORGN]';
> #Have to request the blast with the right amount of alignments, 
> $Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENTS'} = '1000';
> $Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = '1000';
> #and then retrieve it that way as well
> $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'ALIGNMENTS'} = '1000';
> $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'DESCRIPTIONS'} = '1000';
> $Bio::Tools::Run::RemoteBlast::RETRIEVALHEADER{'FORMAT_TYPE'} = 'Text';
> 
> my $r = $factory->submit_blast($inseqfile);
> 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 ) {
>         #This is an error condition, should be a warning or something?
>         $factory->remove_rid($rid);
>       }
>       print STDERR "." if ( $v > 0 );
>       sleep 5;
>     } else {
>       print "Parsing $rid\n";
>       my $filename = parseBlastObject($rc);
>       $factory->save_output($rid, $filename);
>       $factory->remove_rid($rid); 
>     }
>   }
> }
> $factory->DESTROY;
> 
> Mathieu Wiepert
> Medical Information Resources
> Mayo Foundation
> (507) 266-2317 Fax (507)-284-0360
> wiepert.mathieu@mayo.edu 
> 
> 
> 
>>-----Original Message-----
>>From: Damien Mattei [mailto:Damien.Mattei@unice.fr]
>>Sent: Friday, September 13, 2002 6:28 PM
>>To: bioperl-l@bioperl.org
>>Subject: [Bioperl-l] remoteblast result in text format
>>
>>
>>i tried to find since a couple of hours how to retrieve the 
>>basic text 
>>result from a remoteblast , it seems that it was possible in older 
>>version of bioperl but is there a way to get it now? am i missing 
>>something? i know how to get the hits and other things from a 
>>remoteblast but what i need is the same output as the one given by a 
>>standalone blast. Should i have to use the qblast URL API directly ?
>>(http://www.ncbi.nlm.nih.gov/BLAST/Doc/urlapi.html)
>>or bioperl?
>>-----------------------------
>>Damien Mattei
>>C.N.R.S / U.N.S.A - UMR 6549
>>mailto:mattei@unice.fr
>>http://www-iag.unice.fr/
>>-----------------------------
>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l@bioperl.org
>>http://bioperl.org/mailman/listinfo/bioperl-l
>>
> 
> 

----------------------------
Damien Mattei
C.N.R.S / U.N.S.A - UMR 6549
mailto:mattei@unice.fr
http://www-iag.unice.fr/
--------------------------------------