[Bioperl-l] Problems using Bio::Tools::Blast

[gert thijs]

Hello,

I'm trying to write a script to blast several genes with using webblast.pm.
The script should read a fasta file from stdin and blast each sequence
remotely at ncbi. Reading in the sequences is not a problem, but creating the
Blast object is much more trouble. 
I assume I do something wrong in my script but I cannot find what or where. 
Could anyone give me some advice. Code and error message are attached below.


This is my code sofar:
---
$instream = Bio::SeqIO->new(-fh=>\*STDIN, -format=>'Fasta');
%runParam = ( 
	      -prog     => 'blastn',
	      -method   => 'remote',
	      -version  => 2,
	      -database => 'nr',
	      -html     => 'off',
	      -filter   => 'default',
	      -email    => undef,
	      );

while ( $seq = $instream->next_seq() ) {

    $runParam{-seqs} = [$seq];

    # create a BlastObject
    eval { 
	$blast = Bio::Tools::Blast->new(-run=>\%runParam, -parse=>1); 
    };
    if($@) {
        croak "\n*** Trouble creating Blast object:\n$@\n\n";
    }
    print $blast,"\n"; # just for checking

    #$results = $blast->run(\%runParam);
    # here should come some interpretation 
}
---

This script returns the following exception:

-------------------- EXCEPTION --------------------
MSG: Blast file gi_609339_gb_U18675.blastn2.nr.temp.html is incomplete: can't
find program name.
Possibly an unrecognized report format.
CONTEXT: Error in uNKNOWN CONTEXT
SCRIPT: ./ParseBlastReport2.pl
STACK: 
Bio::Tools::Blast::Run::Webblast::_blast(1175)
Bio::Tools::Blast::Run::Webblast::blast_remote(580)
Bio::Tools::Blast::_run_remote(1244)
Bio::Tools::Blast::run(1178)
Bio::Tools::SeqAnal::_initialize(279)
Bio::Root::Object::new(462)
main::./ParseBlastReport2.pl(33)
---------------------------------------------------


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==========================================================
+ Gert Thijs              gert.thijs@esat.kuleuven.ac.be +
+                                                        +
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