[Bioperl-l] remote blast and problem of connection on ncbi

[gregory voisin]

hie, 
presentation: my name is greg , student in bioinformatics at UQAM (montreal)...and i am newbee in perl and bioperl.
i discove with a lot pleasure the world of perl, but these problemes too
 
my problem:
 
i use a script to blast a sequence with remote blast .pm and after motified this module (ligne 168), i have an another problem and my research on google and list od discussion are unsuccessing....
 
when i run my script perl, i have got the message ...""500 can't connect to ncbi.nlm.nih.gov:80 
 
this is my script 
 

use strict;

use Bio::SearchIO;
use Bio::Tools::Run::RemoteBlast;
use Bio::Perl;
use Bio::SeqIO;

#ligne corrigeant le bug du a la ligne 168 dans remoteblast.pm
#info de open-bio bug database
$Bio::Tools::Run::RemoteBlast::RIDLINE = 'RID\s+=\s+(\S+)';

my @inputfiles = @ARGV;

foreach my $inputfile (@inputfiles)

{

my $prog = 'blastn';
#my $db = 'gbEST';
my $e_val= '1e-10';


my @params = ( '-prog' => $prog,
' -data '=> 'est_mouse',
' -expect' => $e_val,
' -readmethod' => ' SearchIO' );


my $factory =
Bio::Tools::Run::RemoteBlast->new(@params);


my $v = 1;
my $chemin ="C:\\Documents and Settings\\voisingreg\\Mes documents\\serveurFTP\\perl\\progPerl\\";

my $str = Bio::SeqIO->new('-file'=> $chemin . "$inputfile",
'-format' => 'fasta');


$Bio::Tools::Run::RemoteBlast::HEADER{'DATABASE'} =
'est_mouse';

$Bio::Tools::Run::RemoteBlast::HEADER{'PROGRAM'} =
'blastn';

while (my $input = $str->next_seq())
{


my $r = $factory->submit_blast($input);


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 {
my $result = $rc->next_result();
#save the output
#my $filename =
$result->query_name()."\.out";
print "$inputfile";

$factory->save_output($chemin . "<$inputfile");
$factory->remove_rid($rid);



}
}
}
}
}


 

thanks for your help 

 

greg



		
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