[Bioperl-l] pb with remote method in Bio::Tools::Blast

[Catherine Letondal]

Hi,

When I run the following code  :

use Bio::Tools::Blast;
use Bio::SeqIO;

# use local program golden from N. Joly to fetch a sequence locally
my $Seq_in = Bio::SeqIO->new (-file   => 'golden sp:TAUD_ECOLI | ', -format => 'swiss');
my $seq = $Seq_in->next_seq();          
print STDERR $seq->seq, "\n";          ###### everything ok until here ######

### the following code is just taken from the Bio::Tools::Blast man page

my %runParam = ( -method   => 'remote',   
		 -prog     => 'blastp',
		 -database =>'swissprot',
		 -seqs     => [ $seq ],  
		 );

print STDERR "running blast...\n";

my $report = Bio::Tools::Blast->new( -run     => \%runParam,
				       -parse   => 1
				       );
foreach my $hit ($report->hits) {
 printf "%s\t %.1e\t %d\t %.2f\t %d\n",
                            $hit->name, $hit->expect, $hit->num_hsps,
                            $hit->frac_identical, $hit->gaps;
}


I get the following error message:

-------------------- EXCEPTION --------------------
MSG: Blast file TAUD_ECOLI.blastp2.swissprot.temp.html is incomplete: can't find program name.
Possibly an unrecognized report format.
STACK Bio::Tools::Blast::Run::Webblast::_blast /local/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast/Run/Webblast.pm:1175
STACK Bio::Tools::Blast::Run::Webblast::blast_remote /local/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast/Run/Webblast.pm:580
STACK Bio::Tools::Blast::_run_remote /local/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1234
STACK Bio::Tools::Blast::run /local/lib/perl5/site_perl/5.6.0/Bio/Tools/Blast.pm:1169
STACK Bio::Tools::SeqAnal::_initialize /local/lib/perl5/site_perl/5.6.0/Bio/Tools/SeqAnal.pm:279
STACK Bio::Root::Object::new /local/lib/perl5/site_perl/5.6.0/Bio/Root/Object.pm:474
STACK toplevel /local/private/sis/letondal/TMP/b.pl:18
-------------------------------------------

Actually, when I look to the file TAUD_ECOLI.blastp2.swissprot.temp.html, there is
nothing regarding the name of the program.

The posting_parameters file looks like this:

Posting address = http://www.ncbi.nlm.nih.gov/blast/blast.cgi

ALIGNMENTS           500
ALIGNMENT_VIEW       0
DATALIB              swissprot
DESCRIPTIONS         500
EXPECT               10
FILTER               default
GENETICS_CODE        1
GI_LIST              (None)
INPUT_TYPE           Sequence in FASTA format
LIST_ORG             
MATRIX               BLOSUM62
NCBI_GI              
OTHER_ADVANCED       
OVERVIEW             
PROGRAM              blastp
SEQUENCE             >TAUD_ECOLI Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17) (2- aminoethanesulfonate dioxygenase) (Sulfate starvation-induced protein 3) (SSI3).
SERLSITPLGPYIGAQISGADLTRPLSDNQFEQLYHAVLRHQVVFLRDQAITPQQQRALA
QRFGELHIHPVYPHAEGVDEIIVLDTHNDNPPDNDNWHTDVTFIETPPAGAILAAKELPS
TGGDTLWTSGIAAYEALSVPFRQLLSGLRAEHDFRKSFPEYKYRKTEEEHQRWREAVAKN
PPLLHPVVRTHPVSGKQALFVNEGFTTRIVDVSEKESEALLSFLFAHITKPEFQVRWRWQ
PNDIAIWDNRVTQHYANADYLPQRRIMHRATILGDKPFYRAG
UNGAPPED_ALIGNMENT   
EMAIL                
HTML                 
PATH                 



Am I doing something wrong?

Thanks,

-- 
Catherine Letondal -- Pasteur Institute Computing Center